Marine Mammal Scientific Research & Enhancement Permit A

OMB No. 0648-0084; Expires xx/xx/xxxx

National Marine Fisheries Service

Marine Mammal Scientific Research and
Enhancement Permit Application
TABLE OF CONTENTS

Table of Contents

INTRODUCTION ...................................................................................................................................... 2
Need help or have other questions? ........................................................................................... 2

When filling out your application: ............................................................................................... 2

APPLICATION INSTRUCTIONS .......................................................................................................... 3
Project Information ........................................................................................................................... 3

Project Description Page ................................................................................................................. 4

Project Supplemental Information ........................................................................................... 14
Captive Information ....................................................................................................................... 18
Project Locations ............................................................................................................................. 20
Take Table .......................................................................................................................................... 20
Anticipated Effects on the Environment ................................................................................ 23
Project Contacts ............................................................................................................................... 26
Submit Application ......................................................................................................................... 28

FREQUENTLY ASKED QUESTIONS................................................................................................ 28
When should I apply? .................................................................................................................... 28
What is the process for getting a permit? .............................................................................. 29

ADDITIONAL INFORMATION .......................................................................................................... 30
PAPERWORK REDUCTION ACT STATEMENT .......................................................................... 30

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Introduction

This application is for requesting a Marine Mammal Protection Act (MMPA) and
Endangered Species Act (ESA) scientific research or enhancement permit to take 1,
import, or export National Marine Fisheries Service (NMFS) protected marine
mammals:
● Cetaceans (dolphins, porpoises, and whales)
● Pinnipeds (seals and sea lions, except walrus)

Need help or have other questions?

We recommend you visit our MMPA scientific research and enhancement permit
web page, see the FAQ on page 27, or contact our office (301-427-8401).

When filling out your application:
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Refer to Chapter 2 for guidance on how to use APPS.

Save your application every 20 minutes or you will lose information!
You do not have to complete your application in one session. Your
application will remain in draft mode until you submit.
An * means it is a required field.

You may want to use these instructions as a template to draft your
application in a Word doc and then cut and paste into APPS. However, note
that special characters may be either lost or migrated incorrectly.
Attachments cannot be larger than 20MB – contact us if you need to attach
larger files.

Your application must be a stand-alone document that describes all proposed
activities and is readable to a layperson.

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A take under the MMPA means to harass, hunt, capture, collect, or kill, or attempt to harass, hunt,
capture, collect, or kill any marine mammal. This includes, without limitation, any of the following: the
collection of dead animals, or parts thereof; the restraint or detention of a marine mammal, no matter how
temporary; tagging a marine mammal; the negligent or intentional operation of an aircraft or vessel, or the
doing of any other negligent or intentional act which results in disturbing or molesting a marine mammal;
and feeding or attempting to feed a marine mammal in the wild.

Under the ESA, a take means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or
attempt to do any of the preceding.
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If you do not follow these instructions, your application will be returned and
you will be asked to resubmit a new application that includes the information
required.
We can only consider those activities that you describe in your application.
We will not consider your application if you have overdue reports for your
most recent permit.

Application Instructions
Project Information

File Number: This number is generated by APPS and cannot be changed. To
facilitate processing, reference this File No. in correspondence with our office.

*Project Title (up to 255 characters): Provide a concise title that includes
activities, species (or taxa if multiple species), location, and purpose of the research.
For example:
● Vessel surveys, sampling, and tagging cetaceans in the Gulf of Mexico to
characterize population structure, foraging ecology, and movement patterns.
*Project Status: The project status (New or Renewal) is automatically selected
based on your answers in the APPS pre-application guide (PAG). Do not change this
field.
Previous Federal or State Permit #: If applicable, enter your most recent and
closely related NMFS permit number. Otherwise leave blank.

*Permits Requested: One or more permits will be listed based on your answers in
the APPS pre-application guide. If the options are incorrect, please contact us at
301-427-8401.
*Where Will the Activities Occur? One or more general locations will be listed
based on your answers in the APPS pre-application guide.

*Research Timeframe: Enter the desired start and end dates of the entire project
in the following format: MM/DD/YYYY. Currently, the maximum duration for an
MMPA scientific research or enhancement permit is 5 years. Please see the FAQ for
details about when to apply.

*Sampling Season/Project Duration (up to 1,000 characters)
Describe the annual field season(s) including the months and frequency of fieldwork
(i.e., when and how many times per year/how frequently will you conduct your
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activities?). If this includes year-round research, indicate when activities are most
likely to occur and how frequently.
*Abstract (up to 2,000 characters): provide a short summary that must include:
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Purpose of the research or enhancement.
Species that may be taken, imported, or exported (common names). If you
are requesting takes of a large number of species, you can list taxa instead of
all species. For example: 20 species of cetaceans and 10 species of pinnipeds.
Proposed activities take activities (e.g., vessel based surveys, remote biopsy
sampling, tagging), import, or export.
Where your activities will occur and where animals or samples will be
imported or to which they will be exported.
Requested duration of the permit (see FAQ).

Project Description Page

*Project Purpose: Hypothesis/Objectives and
Justification (up to 64,000 characters)

We recommend you provide the information in this order:
1. Identify and discuss the research question(s) or
purpose of your project.

2. Briefly summarize published findings related to your
research.
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If you previously held or worked under a research
or enhancement permit, use literature citations
from that support how you previously met your
objectives; and/or
Use other published literature on the subject.

3. Describe how this study is different from, builds
upon, or duplicates past research.

4. If proposing novel procedures, include a discussion
on results from pilot studies or studies on other
species, if available.

Bona Fide Research
The information in your
application should demonstrate
how your proposed research is
bona fide, including how the
results of your research:
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are likely to be accepted for
publication in a refereed
scientific journal;
are likely to contribute to
the basic knowledge of the
species biology or ecology;
or
are likely to identify,
evaluate, or resolve
conservation problems

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5. For ESA-listed and MMPA-depleted species:
• Discuss why your project must involve ESA-listed or MMPA-depleted
species.
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Discuss how your project will, as applicable:
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Contribute to the objectives identified in the species’ recovery or
conservation plan or otherwise respond to recommendations of a
scientific body charged with management of the species;

Contribute significantly to understanding the basic biology or ecology of
the species; and/or
Contribute significantly to identifying, evaluating, or resolving
conservation problems.

If your goals are to directly enhance the survival or propagation of an ESAlisted or MMPA-depleted species, you must also:
• Explain how your project will:
• Contribute to maintaining or increasing distribution or abundance,
• Enhance the health or welfare of the species, and/or
• Ensure the recovery of the species in the wild.

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For captive maintenance for enhancement, explain how you will:
• Maintain a viable gene pool,
• Increase productivity,
• Provide necessary biological information, or
• Establish animal reserves.

How does the benefit of removing animals from the wild into captivity
outweigh alternatives that do not require removal from the wild? What
plans are in place for returning animals and any offspring to the wild?
Justify maintaining animals in permanent captivity.

6. Identify your objectives or hypotheses based on the above information.

7. Take Number Rationale: Explain how you determined your sample size/take
numbers and how they are needed to meet the objectives.

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For example, did you base your numbers on previous encounter rates or
abundance estimates for your study area and the number of surveys to be
conducted?
If appropriate for your study, include a power analysis or other sample
size estimation to show whether the sample size is sufficient to provide
statistically significant or otherwise robust results.
Indicate the number of times known individuals will be intentionally
taken in a year (e.g., recapture for instrument retrieval, multiple biopsy
samples per year, or repeat surveys in the same area for identifiable
individuals). Explain why multiple takes are needed to meet your
objectives.

*Project Description (up to 64,000 characters)
● For work with endangered species, please see our webpage on programmatic
consultations by species group to determine if your methods fall under a
programmatic ESA Section 7 consultation. If you wish to have your work
covered by a programmatic consultation, please ensure that your described
methods fit within its scope. Please contact us if you have questions.
● Provide a brief overview of a day in the field and the suite of activities you
intend to perform on each animal during an encounter or capture event
including where your work will happen, especially if different projects occur
in different locations.

Methods
Describe your methodologies. Your narrative description must match your APPS
take table (see Take Table section below). Every procedure listed in the take table
must be described in the Project Description. It is helpful to reference take table
lines in the narrative that correspond to the take actions and procedures. If you
have multiple projects, it is also helpful to name them by project number or title and
include project names in the Details column of the take table.
You must provide:
● Clear descriptions of all methods (i.e., procedures) for each species (see
examples in Table 1 below).

● A brief statement of each method’s purpose (i.e., how the activity relates to
meeting your objectives).
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● Define how you differentiate age classes (e.g., neonate, calf/pup, juvenile,
subadult, adult). If applicable, distinguish by taxa or species.
● For each method, state if you will target:
o calves/pups (specify age);
o females accompanying calves/pups (specify age); and/or
o pregnant females, and if so, include estimated trimester.

You may attach a table indicating which ages and sex will receive each
procedure if needed (e.g., complex studies or multiple projects).

● For invasive procedures, sensitive life stages (e.g., pregnant females,
calves/pups) should be on separate rows in the take table if they will be
sampled/handled differently to other life stages and can be easily
identified.

● For procedures requiring sterilization and/or disinfection protocols, see the
FAQ for definitions and references.
● Indicate if you will intentionally take an animal more than once per day
and/or year by active acoustics, capture, or invasive procedures.

● If your fieldwork will occur concurrent with other legal takes of marine
mammals (e.g., tagging or sampling an animal following its exposure to an
acoustic trial under another authority), clarify which activities you are
requesting and how they will occur in relation to the other legal action.
Specify how the associated activities are legally covered under the MMPA,
and ESA if applicable.

● Cite references for the methods where applicable, but do not substitute a
literature citation for a complete description of the methods. You can attach
a Literature Cited on the Project Supplemental Information page. References
must be made available upon request.
● On the Supplemental Information page, attach figures and photographs that
illustrate your methods. For example, photos of tags and attachment
methods.
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● Mitigation measures that are inherent to your methods may be included in
this section or in the Effects and Mitigation section below.

Table 1. Guidance for Commonly Used Methods
When describing your methods, be sure to include the following specific
information, as applicable.
Take action/
procedures
Active acoustics

Active acoustics
(for behavioral
response
studies)

Details to include in methods

Sound source (e.g., sidescan sonar, underwater speaker, acoustic
deterrent device)
Source depth in water column
Frequency (bandwidth)
Maximum source level (specify metric SELcum or SPL RMS)
Maximum received level
Distance of source to target and non-target animals
Signal duration and duty cycle
Number of playback sessions in a day and whether you will target the
same animal(s) more than once
Duration of each playback session and maximum total duration of
sound emission per 24-hr period
How many sound source types might be used within a 24-hr period
Ambient sound level, when known
Distance to the relevant 120 dB/ 160 dB re 1µPa Level B Harassment
thresholds and permanent threshold shift (Level A harassment
threshold)
Post playback monitoring (monitoring distance and duration)
We strongly recommend consulting the NMFS 2018 User Spreadsheet
and accompanying instructions. Be sure to specify if your source is
impulsive (direct from source) or non-impulsive (playback via
speaker).

Please include all of the details above in the Active Acoustics section. If
working with a variety of sound sources, be sure to include these
details for a “typical” playback scenario as well as a worst-case
scenario (e.g. source level, received level, duty cycle, frequency etc.).
Make sure to consider all functional hearing groups, including target
and non-target exposures.
Please provide propagation loss model results, when available.

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Take action/
procedures
Administer
drugs or other
substances (e.g.,
stable isotopes)

Aerial and
vessel surveys
(manned)

Aerial surveys
using
unmanned
aircraft systems
(UAS)

Details to include in methods
Name of each drug/chemical and its purpose
Name of any drug reversal
Emergency response and euthanasia drugs and protocols
Dosage of each drug/chemical
Delivery method and route (e.g., dart gun, inhalation, intramuscular,
intravenous, subcutaneous, topical); if dart gun, distance of animal
to water
Location of administration on body
Duration of drug
Personnel that would administer drug (e.g., veterinarian or veterinary
technician; and if they possess any required state licenses)
Post drug administration monitoring
Optional: you may include a drug table with the information
requested above
Type of survey craft and vessel
Number of platforms (aircraft and vessel) to be operated at the same
time
Type of survey (e.g., line transect, photogrammetry)
Number of surveys per year
Minimum altitude/approach distance
Air/vessel speed
Protocols for breaking track to ID species
Duration spent with group or individual/day
Same general questions above for aerial surveys and also the
following:

Type of UAS – fixed wing or vertical takeoff and landing (VTOL)
Payload components – what is the UAS carrying and for what purpose
(e.g., camera, sensor)?
Ground control station description (what it is, where it will be
located-on shore or on vessel, number of stations, and how close the
station will be to animals)
Do you have the appropriate FAA permits/authorizations (including
pilot licenses)?
Encounter duration
Number of platforms (UAS) to be operated at the same time

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Take action/
procedures
Auditory
brainstem
response or
evoked
potential

Capture and
restraint

Export/import
samples

Details to include in methods
Type of measurement equipment (suction cup or needle electrodes)
Type of sounds emitted (e.g., pips, clicks)
Maximum source level
Distance and position from speaker relative to target animal
Signal duration, duty cycle, and frequency of sound emitted
Total duration of sound emission (including total exposure duration
within a 24-h period)
Handling/restraint methods (including anesthesia/sedation, see
above)
Handling duration
Data collection and analysis method
Whether animal will be transported to a facility (complete the
Transport Section in Take Table)
Type of capture (e.g., hand, hoop net, trap) and gear description (e.g.,
net dimensions and mesh size)
Deployment methods (e.g., on foot or boat approach and net
deployment)
Configuration, duration, and monitoring of net sets (how often net set
is checked)
Number of animals captured at a time
Number of animals processed at a time
Anesthesia/sedation (see Administer Drugs above)
Dimensions and type of holding container/manner of restraint
Number and roles of personnel (must be adequate to perform all
activities without harming excess captured animals; else animals
must be released immediately)
Additional equipment or personnel necessary for capturing and
handling excess numbers
Duration of restraint/holding from capture to release
If capturing females with calves/pups, describe how calves/pups
would be held, what procedures would be conducted on the moms
and the calves/pups, duration separated, and how they would be
reunited
Manner of release
Sample type (e.g., blood, muscle)
Where are samples going: person and country
Where are samples coming from: high seas or origin country
Designated port of entry/import or export
How sample/animal is taken in foreign country or on the high seas
and legal take authority
Sample preservation, storage/shipping, and analysis
Re-import/export or retain/archive if samples remain after analysis

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Take action/
procedures
External
instruments
(e.g., external
instruments
attached with
epoxy, suctioncup, dart, or
deep-implants; a
table is helpful
for multiple tag
types)

Details to include in methods
Type of instrument
Location on body
For cetacean deep-implant tags with external instrumentation, please
include the tag penetration depth and describe if the tag is intended
to penetrate the blubber/muscle interface
Dimensions of instrument and attachment
Mass in air or water
Percentage of body mass for all tags combined
Maximum footprint/maximum number of tags/animal
Cleaning/sterile preparation
Attachment method (e.g., remote deployment of suction cup or dart
barb fired from crossbow; restraint and epoxy or harness)
For remote deployment:
● minimum approach distance and angle
● number of attempts per animal/day (i.e., successes and misses)
● include total number of attempts needed for all work if
requesting multiple procedures (e.g., tag and biopsy) on same
animal during same encounter
Whether instrument will be coated with antifouling paint
Whether attachments will be coated with antibiotics
Duration of attachment procedure
Duration of instrument retention on animal
Release mechanism or recapture to remove
Type of data collection (e.g., archival requiring retrieval)
How you determine tag types and number of tags on an animal
Post-tag monitoring

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Take action/
procedures
Internal
instruments
(e.g., stomach
temperature pills,
life history tags,
internal deepimplant tags)

Intrusive
sampling (e.g.,
blood, blubber,
muscle, skin);
remote or under
restraint

Details to include in methods
Type of instrument
Dimensions of instrument
Location within body
For cetacean deep-implant tags with internal instrumentation, please
include the tag penetration depth and describe if the tag is intended
to penetrate the blubber/muscle interface
Mass in air
Percentage of body mass for all tags combined
Cleaning/sterile preparation
Insertion method (describe e.g., surgical implant, injection, stomach
tube, remote deployment)
For remote deployment:
● minimum approach distance and angle
● number of attempts per animal/day (include total number of
attempts needed for all work if requesting multiple procedures
[e.g., tag and biopsy] on same animal during same encounter)
Use of local anesthetic or anesthesia/sedation (see Administer drugs)
Administration of prophylactic antibiotics (see Administer drugs)
Whether attachments or tags will be coated with antibiotics
Duration of insertion procedure
Duration of instrument retention
How instruments are voided
Type of data collection (e.g., archival requiring retrieval)
How you determine tag types and number of tags on an animal
Post-tag monitoring
Type of tissues
Size or volume of sample (diameter and depth or total volume)
Location on body
Number of samples per animal per capture event and per year
Sampling intervals (e.g., for serial blood or biopsy samples)
Equipment (e.g., dart and stopper depth, needle, punch, scalpel)
Equipment sterilization or disinfection
If restrained: cleansing site; left open or wound closure
If remote:
● collection method (e.g., dart fired from rifle)
● minimum approach distance
● number of attempts per animal/day (i.e., successes and misses)
● include total number of attempts needed for all work if
requesting multiple procedures (e.g., tag and biopsy) on same
animal during same encounter
Sample preservation, storage, and analysis

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Take action/
procedures
Marking (e.g.,
bleach, flipper
tag, freeze brand,
hot brand, paint,
PIT tag)
Non-intrusive
sampling (e.g.,
behavioral
observations via
focal follows and
ground surveys;
breath sampling;
collecting
molt/scat/spew;
passive acoustic
monitoring;
photo-ID;
photogrammetry;
remote video
monitoring;
underwater
photography)
Remotely
operated
vehicle (ROV),
vessel or
amphibious

Details to include in methods
Type of mark
Number of tags or brands
Location on body
Method of application
Disinfection procedures
Duration of mark (e.g., until molt)
Whether marks would be reapplied, if lost
Dimensions of tag or mark
Total number and combination of tags or marks on each animal
Approach method
Sampling method
Minimum and maximum approach distance
Within sight of animals or not (e.g., from a blind)?
Frequency of observations/sampling
Number of approaches per animal/day for biological sampling
Duration of observations/sampling/day
Data or sample collection and analysis
If conducting underwater photography/videography, specify the
method (e.g., snorkeling, underwater pole cam, or divers that could
use typical gear or rebreathers) and number of individuals in the
water at a given time, including safety divers

For underwater and amphibious ROVs, same details as for vessel
surveys and also:

Description and size of ROV
Whether it is tethered or wireless, tether material and length
Deployment method, in relation to capture and release of animal, if
applicable
Describe any light sources
Whether there will be a live video feed monitored
Encounter duration

Non-target Marine Mammals:
Discuss whether and how non-target marine mammals may be incidentally
harassed, captured, or otherwise affected. These are species that co-occur with your
target species and that could be harassed or taken during your research. Include
these on separate rows in the Take Table if you expect incidental take (e.g.,
harassment or capture). For ESA species designated by DPS, specify the DPSs.
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Non-target taxa (e.g. sea turtles, seabirds) should be addressed in the Effects and
Mitigation section below.

Project Supplemental Information

Attach a Supplemental Information File
You can attach up to 10 files to provide additional information.
● Preferred file formats: Microsoft Word, Excel, or PDF.
● The maximum file size allowed is 20 MB.
● Audio and video files (such as mp3, m4b, wav) cannot be uploaded. Contact
us if you need assistance.
● On the Location screen you will be asked to attach a map.
Status of the Affected Species (up to 2,000 characters)
If choosing “range-wide” in the Stock/Listing Unit column in your take table,
indicate which stocks or DPSs you are targeting.

*Mortalities (up to 2,000 characters)
If authorization for serious injury 2 or mortality 3 (euthanasia/intentional4 or
accidental/unintentional) is proposed:
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What activities could result in mortality?

Briefly summarize mortalities that have occurred during the previous five
years of your permitted activities using the same or similar techniques;
include circumstances and cause of death, and how a similar outcome can be
prevented.
Explain why it’s not feasible to use other methods that won’t result in
mortality.

A serious injury is an injury that will more likely than not result in mortality.

3

Caused by the presence or actions of researchers including but not limited to deaths or serious injuries
sustained during capture and handling, while attempting to avoid researchers or escape capture, or resulting
from infections related to intrusive procedures such as sampling or tagging. This does not include a fetus if
a pregnant female dies.

4

This includes euthanasia for humane reasons (e.g., due to serious injury during research).
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If authorization for mortalities of ESA-listed or MMPA-depleted species is
proposed, explain how the research or enhancement will directly benefit the
species or fulfill a critically important research need.

What is the maximum number of animals of each species/DPS that could be
seriously injured, unintentionally die, or be euthanized annually and over the
life of the permit? For example, 10 mortalities across the life of the permit,
not to exceed five mortalities in any one year.
Justify the number of mortalities.

How is euthanasia decided, conducted, and who conducts it?

What are the protocols for necropsy and carcass disposal? If necropsy
cannot occur, explain why.
What are the protocols for disposition of dependent pups or calves if
lactating females may die as a result of your actions?

*Effects and Mitigation (up to 64,000 characters)

Discuss how Take Action, Observe/Collect Method, and Procedure, except
mortalities, in the take table will affect target and non-target animals. Effects of
mortalities only need to be discussed above in the Mortalities section.

Cite the best available science (i.e., peer-reviewed literature or other published
data sources) and your experience (e.g., personal communication). References must
be made available upon request.
For each method and take action include:
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Typical behavioral and physiological responses,
Worst-case responses,
% of animals that exhibit each response type,
Average/estimated recovery time, and
Wound healing time.

Also include an assessment of:
● Condition of animals on recapture/resight
● Recovery from sedation and handling
● Post-release behavior (immediate and long-term)
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Time to repopulate rookeries/haul outs after flushing
Healing from intrusive sampling
Healing from intrusive tag deployments
Tag retention
Effects to lactating females and their dependent young

For novel procedures, discuss the most likely anticipated responses based
on literature from studies on other species, if available, and any results from
testing, if applicable.
Discuss the anticipated effects on the species or stock, especially if
mortalities or reproductive effects are possible. On what is your
determination based?

You may include mitigation and monitoring protocols here, or in the Project
Description section. Do not restate them here if they are included above; simply
reference the section where the following information is found.
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6

Describe if you will employ mitigation measures when you observe
unintended adverse reactions. If you will take the same measures for a
suite of activities, such as those resulting in Level B harassment vs Level A
harassment, you may provide one discussion for each suite.

Describe your short- and long-term post-procedure monitoring protocols.

Explain why monitoring or mitigation is not feasible for specific procedures,
species, situations, etc. as needed.

Humane 5 determination: Explain how you determined your methods
involve the least possible degree of pain and suffering possible and why
there are no feasible alternative methods to obtain the desired data or
results.

Where an IACUC (Institutional Animal Care and Use Committee) review is
required 6, to support a humane determination under the MMPA and
compliance with the Animal Welfare Act, attach

Humane means using the method that involves the least possible degree of pain and suffering possible.
Any marine mammal research that involves an invasive procedure, and which can harm or materially alter
the behavior of the animals under study requires an IACUC review and approval. If an applicant does
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the IACUC protocols submitted
● any IACUC comments or recommendations
● the signed IACUC approval (or status of your application)
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Please describe any mitigation you will take to avoid or minimize impacts to
non-target protected species (e.g., sea turtles, corals, USFWS species). Discuss
whether and how they may be incidentally harassed, captured, or otherwise
affected. For ESA species designated by DPS, specify the DPSs. Identify if you
require takes of these species.

Research Coordination:
● Describe how you will collaborate or coordinate with other researchers in
your action area.
●

List these researchers and their institutions and explain how you will work
together. For example, will you share vessels, samples, or data? Will you
coordinate the timing of surveys to avoid repeated take of the same animals?

Attach a References File
Attach a bibliography of references cited in this application. Referenced materials
must be made available upon request, as needed for evaluation of the application, or
preparation of any necessary ESA or NEPA analyses. If a link to your referenced
material is available, add the link to your References File.
*Resources Needed to Accomplish Objectives (up to 2,000 characters and attach
files if necessary)
● Explain how your expertise, facilities, and resources (people, physical, and
monetary) are adequate to accomplish your proposed objectives and
activities.
●

●

Attach copies of relevant formal research proposals, contracts, grant awards,
or letters of agreement that would demonstrate financial or logistical
resources.
Indicate the status of other international, federal, state, or local
authorizations and permits you have applied for, secured, or will apply for.

not have an IACUC, an alternate IACUC (e.g., of a Co-Investigator or a local university/research
institution) may be used.
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*Disposition of Tissue Samples (up to 2,000 characters)
Indicate the disposition of any remaining samples after your project is complete.
●

●

State whether samples will be consumed in analysis, destroyed,
retained/archived, or returned to a facility/researcher.

List the name and location of any person or institution that will
store/curate/receive samples. Indicate if you will retain legal custody of the
archived samples or if you wish to permanently transfer the samples once
your project is complete.

*Public Availability of Product/Publications (up to 800 characters)
Describe the end products of your proposed project and how they will be made
available to the public.

Captive Information

If you will be working with animals in captivity (permanent or temporary),
including removing animals from the wild into captivity and research or
enhancement on captive or rehabilitating animals, address the following (explain if
not applicable):
1. If removing animals from the wild, explain why removal is necessary and
why you cannot obtain suitable animals from captive or rehabilitated stock.
2. If the animals are beached/stranded marine mammals undergoing
rehabilitation, indicate the name and location of the rehabilitation facility.

3. If the animals are already in captivity (other than animals in rehabilitation)
indicate the name and location of the facility and, where possible, identify the
specific animals (by NOAA ID number if applicable).
4. Attach a copy of any license or registration issued by the Animal and Plant
Health Inspection Service (APHIS) of the U.S. Department of Agriculture, any
outstanding variances granted, and the most recent APHIS inspection report.
5. Attach the protocol forms submitted to the appropriate Institutional Animal
Care and Use Committee (IACUC) established under the Animal Welfare Act
(AWA), the IACUC approval, and any comments and recommendations of the
IACUC.
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6. Attach a written statement from the responsible veterinarian or expert
certifying that the facilities, methods of care and maintenance, and methods
of transport will be adequate to ensure the well-being of the animals and will
comply with all care and transport standards established under the AWA.

7. Describe the care and maintenance of the animals, including a complete
description of the facilities where they will be maintained. This includes:
● dimensions of the pools or other holding facilities
● water supply, amount, and quality
● sanitation practices
● number, sex, and age of animals by species to be held in each
● quarantine procedures and acclimation plan for introducing new and
currently held animals and contingency plans if adverse responses are
observed
● diet, amount and type.

8. Will a captive breeding program be established? If so, provide justification in
accordance with the species conservation plan or recovery plan. For ESAlisted marine mammals, indicate if you are willing to participate in a captive
breeding program if requested by NMFS.
9. Indicate the disposition of captive animals at the end of your research or
enhancement activities.

10. If you’re proposing to release of captive animals into the wild, state how long
the animals will be held, no matter how temporary. Describe the protocols
for the release, which must include:
●
●
●
●

post-release monitoring protocols
disease transmission between released animals and the wild population
potential genetic exchanges between introduced and endemic stocks
ability of the released animals to forage and protect themselves from
predators
● elimination of behavioral patterns acquired during captivity that could
prove detrimental to the released animals or the social structure of local
populations.
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Project Locations

First, describe where you plan to work. Then, for
each location, use the Take Table to list the
species you expect to encounter and the
procedures you will conduct.
●

●

●

Add New Location: provide information
about one or more study areas
● General area (ocean basin)
● State(s), as applicable.

Enter Location Details, as applicable:
● Waterbody: enter names of rivers,
estuaries, bays, etc.
● Latitude and longitude of your
study area
● River miles (Being Mile and End
Mile)
● Limits of your study area (e.g., to the
U.S. EEZ, to the edge of the
continental shelf, to 50m depth)
● Names of land masses where
research will occur (e.g., islands,
rookeries).
Attach File: Include a high quality map(s)
to scale that clearly shows the location of
your proposed activity and any
environmental areas of interest. If
possible, include a shapefile, Google Earth
kmz/kml, or ASCII text file with lat/long
data and the associated basic metadata
with your application.

Take Table

The take table represents the estimated number
of animals you proposed to take annually during
your research.

How to count takes
of pinnipeds

Count 1 take per animal per day
for those hauled-out animals
that react to the research,
regardless of the number of
responses, including:
• movements of twice the
animal’s body length or
more,
• changes of direction greater
than 90 degrees, or
• retreats (flushes) to the
water.
Count 1 take per animal per day
for those animals in water that
exhibit a noticeable adverse
behavioral response from your
activities

Do not count alert behaviors
such as:
• turning head towards the
disturbance,
• craning head and neck while
holding the body rigid in a ushaped position,
• changing from a lying to a
sitting position, or
• brief movements of less than
twice the animal’s body
length.

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Columns you will fill out in the take table:

1. Select: Leave this box blank unless you need to
copy, move, or delete the row.

2. Species: Use the drop down list.

3. Listing Unit/Stock: Select the applicable MMPA
stock or ESA listing unit. Choose Range-wide if
your location has multiple stocks of the same
species and you cannot distinguish between
them while in the field.
4. Production/Origin: Select from the drop-down
list. Categories include Wild, Captive,
Rehabilitation Facility, or All.

5. Life Stage: Select from the drop-down list. You
may enter take information for more than one
life stage (e.g., adult versus juvenile) on separate
rows or select a combination of life stages for
one take category.
6. Sex: Select from the drop-down list. If your
suite of activities targets only one sex, indicate
which. Otherwise select Male and Female.

7. Expected Take: This represents a reasonable
estimate of the maximum number of individuals
you will take, import, or export, annually.

8. Take Action: The “take action” is a generalized
overview of how animals will be taken by your
activities over the course of the year. If more
than one action is proposed for your project, you
must enter the takes on separate rows.
9. Observe/Collect Method: Select the method of
observation (e.g., survey, vessel) or
collection/capture. Select only one
observe/collect method per row.

How to count
takes of
cetaceans

Count every animal
approached regardless of
whether a behavioral
reaction has occurred.

During vessel surveys, only
count 1 take per animal per
day including all
approaches. An “approach”
is defined as a continuous
sequence of maneuvers
involving a vessel,
equipment, or researcher’s
body, including drifting,
directed toward a cetacean
or group of cetaceans closer
than 100 yards for baleen
and sperm whales and 50
yards for all other cetaceans.

During aerial surveys
(manned or UAS) flown at an
altitude lower than 1,000
feet, count 1 take per animal
observed per day, regardless
of the number of passes over
the same animal.

10. Procedures: Provide specific information on the research activities that you
will conduct. A separate pop-up window will appear with a species-specific
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list of activities. Hold down the Control key to
select all activities to be performed
concurrently.
a. Choose Other if your proposed activity
is not listed. In the Details box (see
below), briefly describe what the
Other means.

b. If some animals will only get a subset
of procedures, list this subset on a
separate row in the take table. List out
the suite of procedures that will be
performed only on a subset of animals
in the Project Description and explain
how you decide which animals receive
which procedures.

Acoustic Playbacks
For acoustic playback trials in
the wild, estimate take for each
target and non-target species
based on the isopleth distances
that result from the following
thresholds:
•

11. Transport: If you chose Transport as a
Procedure, enter information about the
transport when prompted.

a) Mode(s) of transportation: Describe the
mode of transportation. Include a description
of the vehicle or other platform used to
transport animals.

b) The name of the transportation company, if
applicable, and the qualifications of the
common carrier to transport live animals: If a
contractor or other entity will do the
transportation, enter information in the box.
Otherwise, click on N/A.
c) Maximum length of time from capture to
arrival at destination: How long will the
animals be in transport?

•

Level B harassment
behavioral threshold of a
received level of 120db re
1µPa (continuous sounds)
and 160 dB re 1µPa
(intermittent sounds), and

Level A harassment
threshold for permanent
threshold shift (injury).
This varies by functional
hearing group. Refer to our
acoustic guidance at:
https://www.fisheries.noaa.
gov/national/marinemammalprotection/marinemammal-acoustic-technicalguidance

d) Description of the container (e.g., cage, tank) used to hold the animal
during transit: Include the material of the container and its dimensions.

e) Any special care procedures (e.g., moisture, medicines) to be administered
during transport: How will the animals be cared for during transport?
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f) A statement as to whether the animals will be accompanied by a
veterinarian or some similarly qualified person: If so, give the name,
affiliation, contact information for each person.

g) Destination: Use the drop down list to select the destination. If your
destination is not on the list, click on the “New Facility” button to add it. If
the animals will be taken to a laboratory or aquarium, provide details of the
location. If the animals will be released in another waterbody, provide
details of the location.

h) How will the animals be contained at the destination facility?: Discuss the
quarantine procedures. Describe the quarantine and permanent holding
spaces, including effluent treatment.
i) The final disposition of the animals: Describe, for example, whether the
animal will be released or retained in permanent captivity.

12. Begin Date: Populated with the Begin Date you entered on the Project
Information page. You may change the date to coincide with a specific
project time shorter than the overall duration of the project. You cannot
enter a date that is earlier than your original Begin Date.

13. End Date: Populated with the End Date you entered on the Project
Information page. You may change the date to coincide with a specific
project time shorter than the overall duration of the project. You cannot
enter a date that is later than the End Date you previously entered.

14. Details (Optional): You may enter up to 255 characters in this text box to
provide details on each take table line. This is especially useful for clarifying
age class, takes, intentional repeated takes (e.g., recapture for instrument
removal), endangered DPSs where mixing occurs, specific activities, or
projects.

Anticipated Effects on the Environment

1. Will you be working in or near areas with unique environmental
characteristics or important scientific, cultural or historical resources?
Examples include:
•

Animals used for subsistence

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•
•
•
•
•
•
•
•
•
•
•
•
•

Archaeological resources
Critical Habitat of ESA-listed species
Essential Fish Habitat including wetlands, coral reefs, sea grasses, and
rivers
Federally recognized Tribal and Native Alaskan lands, cultural or natural
resources, or religious or cultural sites
Marine Protected Areas
Minority or low-income communities
National or State Parks
National Marine Sanctuaries and National Monuments
National Historic Landmarks
Sites listed in or eligible for listing in the National Register of Historic
Places
Wild and Scenic Rivers
Wilderness Areas
Wildlife Refuges

a. If yes, please list those areas. As applicable, mention if you will need to or
have already obtained permission (licenses, permits, authorizations) to
work in these areas.
b. How would your activities affect such resources? What measures will
you take to ensure your work does not cause loss or destruction of such
resources?
c. For marine mammal activities in Alaska or Washington, how will you
ensure your project does not adversely affect the availability (e.g.,
distribution, abundance) or suitability (e.g., food safety) of marine
mammals for subsistence uses?

2. Discuss if your activities have the potential to impact the physical or
biological environment, in particular coastal and marine environments.
Impacts can be positive or negative. Examples of potential impacts include:
•
•
•
•
•

Altering substrate while anchoring vessels and buoys.
Using bottom trawls or other types of nets.
Erecting blinds or other structures.
Ingress and egress of researchers.
Injuring or killing benthic organisms (e.g., sea grass, corals).
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•
•

Altering the physical or chemical characteristics of water (e.g., oil
spills)
Affecting a species’ abundance or distribution.

3. Does your project involve activities known or suspected of introducing or
spreading invasive species, intentionally or not? Examples include
transporting animals or other biological specimens, discharging ballast
water, and using boats/equipment at multiple sites.

Describe measures you would take to prevent the possible introduction or
spread of non-indigenous or invasive species, including plants, animals,
microbes, or other biological agents.
4. Will your activities involve collecting, handling, or transporting potentially
infectious agents or pathogens, such as biological specimens (animals, blood,
tissues)?

Will your activities involve using or transporting hazardous substances, such
as toxic chemicals?
If yes to either question, describe the protocols you will use to ensure that
public health and human safety are not adversely affected, such as by spread
of zoonotic diseases, chemical injuries, or contamination of food or water
supplies.

5. Do your activities involve equipment (e.g., scientific instruments) or
techniques that are new, untested, or have unknown or uncertain impacts on
the biological or physical environment?
If yes:

a. Briefly describe the equipment or techniques and provide any
information about the use of these in your study area, other areas,
and/or with other taxa.

b. Discuss the degree to which they are likely to be adopted by others for
similar activities or applied more broadly.

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Project Contacts

As the person entering the application, you will automatically be assigned the
following roles: Applicant/Permit Holder, Principal Investigator, and Primary
Contact.
1. You may need to change or add personnel. See Chapter 2 for directions on
how to change who is assigned to these roles.
2. Use the guidance below to help you decide who should have what role.
3. To prevent duplicate entries, ALWAYS search APPS for the person before
entering a new contact. Start with only putting the last name in APPS
search box.
4. Include a table (see example Table 2) listing the names of the PI and CIs, and
the specific procedures they will oversee or conduct. Attach the table on
the Supplemental Information page.
5. As you add personnel, check whether each person already has a
Qualifications Form (QF) in APPS. It will appear next to their name once
you add them to your Contacts page. If there is not a QF in APPS, then attach
one for the PI and each CI. See Qualifications and Experience below.

Descriptions of Personnel Roles
A project must have a Responsible Party if the Applicant/Permit Holder is an
organization, institution, or agency. The Responsible Party or Applicant/Permit
Holder is an official who has the legal authority to bind the organization, institution,
or agency and is ultimately responsible for the activities of any individual operating
under the authority of the permit.

The Principal Investigator (PI) is the individual primarily responsible for the take,
import, export, and any related activities conducted under the permit. There can
only be one PI on a permit. The PI:
● Must have qualifications, knowledge, and experience relevant to the activities
authorized by the permit
● Must be on site during activities conducted under the permit unless a CoInvestigator is present to act in place of the PI
● May also be the Applicant/Permit Holder and Primary Contact.
The Primary Contact is the person primarily responsible for correspondence
during the application review process and after a permit is issued. Typically this
person administers the permit, requests amendments/modifications (e.g., personnel
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changes, filming requests), and submits reports. The Primary Contact may also
serve other roles on the permit (e.g., Applicant/Permit Holder, PI, CI).

The Applicant/Permit Holder or Responsible Party, PI, and Primary Contact
will have access to APPS to enter and edit the application, submit reports and
modification requests, and will receive automatic emails from APPS.
Co-Investigators (CIs) are individuals who are qualified and authorized to conduct
or directly supervise activities conducted under a permit without the on-site
supervision of the PI.
● You may add CIs to the application if the PI will not always be present during
the permitted activities.
● CIs can also be added or removed once a permit has been issued.

Research Assistants (RAs) are individuals who work under the direct and on-site
supervision of the PI or a CI. RAs cannot conduct permitted activities in the absence
of the PI or a CI. RAs do not need to be named in the application or permit.
Authorized Recipients (ARs) are persons or institutions authorized to receive
samples for analysis or curation related to the objectives of your permit as
discussed in the Disposition of Tissues section. Permit holders may designate ARs
at their discretion with a letter. ARs do not need to be identified in the application
or permit.

Qualifications and Experience
The PI and each CI must have a Qualifications Form (QF). Previously we accepted
CVs, resumes, and biosketches, but often these did not include sufficient information
about the person’s field experience. The QF is designed to give us the information
we need. Once you fill out a QF and attach it to your profile in APPS you won’t have
to do it again, unless your skills or experience change. Each contact should only
have 1 QF file in their profile; they may replace the existing file with an updated
version as they gain new experience.
Persons authorized as the PI or CIs must have qualifications corresponding to their
duties. Note, if the PI or a CI will be supervising but not performing specific
procedures, each person must have sufficient cumulative experience to oversee the
project, personnel (e.g., other CIs, research assistants, veterinarians), and
procedures.
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If you do not provide sufficient information, we will not authorize the person(s) to
conduct the research or enhancement activities.

In addition, you must submit a table (see Table 2) defining the roles and activities to
be performed for the PI and each CI listed in the application.
Table 2. Example Personnel Roles
Name/Affiliation
Role
John Smith, Ph.D.,
Principal Investigator
University A, City,
State
Jane Smith,
Co-Investigator
Institution B, City,
State
Mary Smith,
Co-Investigator and
D.V.M., Institution Attending Veterinarian
B, City, State
Jane Doe, Ph.D.,
Co-Investigator
Institution C, City,
State
John Doe, Ph.D.,
Co-Investigator
University D, City,
State
Bob Smith, City,
UAS pilot
State

Activities
Supervise all activities under the
permit; conduct all activities
except anesthesia
All activities excluding UAS and
anesthesia during captures and
UAS
Oversee and conduct anesthesia
and all biological sampling
during capture activities
Conduct photo-ID
Collect remote skin/blubber
biopsy samples and create cell
lines
UAS pilot

Submit Application

See Chapter 2 for how to submit your application and check on its status.

Frequently Asked Questions
When should I apply?

MMPA permits (no ESA-listed species): at least 6 months before your project
will begin.
● ESA-MMPA permits: it depends on the species and activities you are
proposing
● Pinnipeds – at least 1 year before your project will begin.
● Cetaceans – your project may fall under our programmatic
consultation, which means you should submit your application 6
months prior to starting work, and following our application cycle. If
●

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your proposed research is not covered under a programmatic, then
you need to apply at least 1 year before your project will begin.
● Note: If you are requesting deep-implant tags for ESA-listed cetacean
species, you must apply on the cycle indicated on our programmatic
webpage if you wish to be covered by the programmatic consultation.

How are disinfection and sterilization defined?

Disinfection eliminates many or all pathogenic microorganisms, except bacterial
spores, on inanimate objects usually by liquid chemicals (CDC 2008).

Sterilization destroys or eliminates all forms of microbial life and is carried out by
physical or chemical methods (CDC 2008).

What is the process for getting a permit?

1. Follow these instructions and contact the Permits and Conservation Division
at 301-427-8401 with any questions.
2. Submit your application via APPS.
a. A permit analyst will review your application and contact you if
additional information is needed.
3. Address any questions within 60 days or your application will be withdrawn.
a. Once we consider your application complete, we will publish a notice
in the Federal Register, which starts a mandatory 30-day public
comment period.
b. Concurrently, we will send your application to the Marine Mammal
Commission and other subject matter experts in partner institutions
and federal and state agencies for review.
c. We will determine whether or not your proposed research requires
an ESA Section 7 consultation. Your research may fall under a
programmatic consultation. If it does not follow under the
programmatic, we will need to request consultation to assess impacts
to ESA-listed species. The ESA consultation can take up to 6 months.
4. Address any questions received during the comment period.
a. We will draft the permit and supporting documentation (including
National Environmental Policy Act analyses and documentation of
MMPA and ESA issuance criteria).
b. The documents will be reviewed by various NMFS offices including a
legal review.
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c. For individual consultations, a Biological Opinion will be issued if
ESA-listed species may be taken and adversely affected to determine if
the activity will jeopardize the species or adversely modify critical
habitat.
d. The Office Director will decide whether to issue or deny your permit.

What is the process for requesting an amendment to a permit?

Use APPS to request an amendment to your permit. You’ll need to provide a
description of your proposed changes and include all the necessary details for those
changes, as applicable. Use these application instructions as a guide. For example,
changes to your objectives will require that you discuss all the points in the Project
Purpose section. Additions to personnel require Qualifications Forms and
descriptions of their roles.

Additional Information

Under Section 104(c) of the MMPA and Section 10(a)(1)(A) of the ESA, persons may
be authorized to take marine mammals and threatened and endangered species,
respectively, for purposes of scientific research or enhancing the survival of the
species. Interested persons are required to submit an application in accordance
with the Acts and the implementing regulations at 50 CFR Part 216, subpart D, and
50 CFR Part 222. These instructions for applying for a research or enhancement
permit are drawn from, but do not substitute for ESA regulations and MMPA
regulations. Read the full text of the MMPA, including Section 104. Read the full text
of the ESA, including Section 10(a)(1)(A). Under NEPA, Federal agencies must
assess the effects of federal actions on the environment. Under Section 7 of the ESA,
Federal agencies must ensure that the permitted activities will not jeopardize the
continued existence of the species or result in adverse modification of critical
habitat.

Paperwork Reduction Act Statement

The information requested in this application is required and is used to determine
whether the activities described in the application are consistent with the purposes
and policies of the Acts and their implementing regulations.
Public reporting burden for this collection of information is estimated to
average 50 hours per response, including the time for reviewing instructions,
searching existing data sources, gathering and maintaining the data needed, and
completing and reviewing the collection of information. Send comments regarding
this burden estimate or any other aspect of this collection of information, including
suggestions for reducing this burden, to the Chief, Permits and Conservation
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Division, Office of Protected Resources, F/PR1, NOAA/National Marine Fisheries
Service, 1315 East-West Highway, Silver Spring, MD 20910.

All permit documentation, including the application, permit and amendments,
reports, inventory information, and any other associated documents are subject to
the Freedom of Information Act.

Notwithstanding any other provision of the law, no person is required to respond to,
nor shall any person be subject to a penalty for failure to comply with, a collection of
information subject to the requirements of the Paperwork Reduction Act, unless
that collection of information displays a currently valid OMB Control Number.

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