Application Instructions for a Permit for Scientific Pur

OMB Control No. 0648-0402

Expiration Date: 02/28/2009

National Marine Fisheries Service (NMFS)
Application Instructions for a Permit for Scientific Purposes
or to Enhance the Propagation or Survival of Threatened and Endangered Species
Authority
Under section 10(a)(1)(A) of the Endangered Species Act of 1973 (ESA), National Oceanic and
Atmospheric Administration (NOAA)’s National Marine Fisheries Service (NMFS) may issue
permits for scientific research purposes or to enhance the propagation or survival of species
listed as threatened or endangered under the ESA. The authorization provided by these permits
exempts the permit holder from the prohibitions of ESA section 9, in particular those dealing
with take. Take is defined by the ESA as: "to harass, harm, pursue, hunt, shoot, wound, kill,
trap, capture, or collect, or to attempt to engage in any such conduct." Permitted activities must
not operate to the disadvantage of the listed species and must provide a bona fide and necessary
or desirable scientific purpose or enhance the propagation or survival of the listed species.
NMFS traditionally issues permits for up to five years, although permits for longer periods of
time have been issued. Permits include any conditions necessary to mitigate and monitor the
impacts of the proposed activities. These application instructions are drawn from, but do not
substitute for, the ESA section 10 regulations at 50 CFR §222.308. Applicable state laws or
regulations prevail in all cases where they are more restrictive. Possession of a section
10(a)(1)(A) permit should be regarded as a privilege in that NMFS must balance permit issuance
with its duties to protect and recover listed species.
Do I Need to Apply for a Permit?
If you determine that your proposed activity would directly take a listed species (i.e., the listed
species is the subject of your proposed activity, and conducting it would likely result in the
species being harassed, captured, harmed, possessed, or killed) and your planned activity is
otherwise lawful, a section 10 (a)(1)(A) permit is required. Examples of activities that may
require a section 10 (a)(1)(A) permit include: surveys, genetic research, hatchery operations,
relocations, capture and marking, and telemetric monitoring. Under certain circumstances, a
section 10(a)(1)(A) permit may also be required for you to possess listed species’ tissues or body
parts.
If you are engaged in an otherwise lawful activity where a listed species may be adversely
affected, and the purpose of your activity is not scientific research or species enhancement, you
may need to obtain a section 10(a)(1)(B) permit (Incidental Take Permit). Examples of activities
that may require a section 10(a)(1)(B) permit include: state sportfishing programs, non-listed
fish stocking programs, and other instream or watershed activities which may affect listed
species. If your proposed activities require an incidental take permit, you will need to use the
section 10(a)(1)(B) instructions. These are available at the addresses listed below under Where
Do I Send the Application? and at the NMFS Office of Protected Resources web site,
http://www.nmfs.noaa.gov/pr/permits/esa_permits.htm
Section 4(d) authorizations are available for research and monitoring that may affect threatened
Pacific marine and anadromous fish (http://www.nwr.noaa.gov/ESA-Salmon-Listings ). State
agencies screen all research applications and then work with NMFS to ensure authorized
research does not over utilize the resource. You can find more information on how to apply for a
section 4(d) permit at the following NMFS web site: http://www.nwr.noaa.gov/ESA-SalmonRegulations-Permits/4d-Rules/Index.cfm.
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Other state issued collecting permits are available that vary by their restrictions and
qualifications. To determine whether your activities can be covered by one of these permits go to
your state agencies website below:
The Oregon Department of Fish and Wildlife (ODFW) has requirements for Scientific Collecting
Permits and Incidental Take Permits. Information regarding these requirements and the
application process is available at the following web site:
http://www.dfw.state.or.us/fish/license_permits_apps/.
The California Department of Fish and Game (CDFG) has requirements for Scientific Collecting
Permits and Incidental Take Permits. Information regarding these requirements and the
application process is available at the following web site:
http://www.dfg.ca.gov/wildlife/research_permit/.
The Idaho Department of Fish and Game (IDFG) require a permit for scientific collecting. The
application for this permit can be acquired at the following web site:
http://fishandgame.idaho.gov/cms/licenses/apps/collect_permit.pdf.
The Washington Department of Fish and Wildlife (WDFW) has requirements for Scientific
Collection Permits. Information about these requirements and the application are available at the
following web site: http://wdfw.wa.gov/scp/.
If you still have questions, you may want to consult the Pre-Application Guide (PAG) on the
Authorizations and Permits for Protected Species website. The PAG will walk you through a
series of questions to help you determine what type of permit you need and whom you should
contact. The PAG can be found at http://apps.nmfs.noaa.gov/.
Before applying for an individual permit, you should determine if your proposed project is a part
of another authorized activity. To minimize duplication—and the impact on listed species—you
are strongly encouraged to coordinate with others doing similar work. If two investigators are
collaborating on the same activities, they should apply for a single permit. Also, if you are
conducting your proposed activities in response to a Federal Agency requirement, you may not
need a section 10 (a)(1)(A) permit. For example, fish surveys required by an ESA section 7
biological opinion may be authorized in the opinion’s Incidental Take Statement and no section
10 permit would be needed.
Am I Using the Appropriate Application Instructions?
These instructions are for permits for research and/or enhancement activities involving listed
Pacific salmon and steelhead. They can be downloaded from:
http://www.nmfs.noaa.gov/pr/permits/esa_permits.htm
Permits for marine mammal species and non-salmonid threatened and endangered species (e.g.,
shortnose sturgeon, sea turtles, white abalone), please use the application instructions available
at: http://www.nmfs.noaa.gov/pr/permits/
For terrestrial or freshwater species, or land-based sea turtle activities, please contact the
appropriate regional office of the U.S. Fish and Wildlife Service:
http://www.fws.gov/endangered/permits/permitscontacts.html
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When Should I Apply?
To allow for processing time, you are urged to apply at least six months before you need to start
your proposed activities, however certain permit actions may take even longer to process.
What Should I Include in the Application?
A permit application should provide all of the information requested below and, for processing
efficiency, it should be displayed in the same structure and format. We will use the information
that you provide to determine whether your application is complete and whether to issue a permit
for the proposed activities. If a section does not apply to your activities, please indicate this by
including a header for that section followed by N/A. Applicable information should be detailed
enough to provide a complete picture of your proposed activities. Incomplete or vague
information will delay processing. Please note that specific wording is required for the closing
statement. If you already have a project proposal, you may attach the proposal and reference the
appropriate sections of it when filling out your application.
Should I Send a Review Draft?
It is often helpful to draft an application and send it to us for review before mailing your final
application. Send the draft electronically (contact the appropriate office for a current email
address). Our staff will review your application and help you if there are any difficulties. Once
the application is complete, you must send a signed copy to the appropriate office.
Where Do I Send the Application?
Mail one signed original of the complete, final application to the appropriate address below.
You should also submit a copy by e-mail to help speed processing. If you need help completing
your application, submit a draft to the appropriate office or contact them directly.
Permits for marine and anadromous species in the Pacific Northwest:
Chief, Protected Resources Division
National Marine Fisheries Service - F/NWO3
1201 NE Lloyd Boulevard, Suite 1100
Portland, Oregon 97232-1274
Phone: 503-736-4721
Fax: 503-230-5441
Permits for marine and anadromous species in California:
Protected Resources Division
National Marine Fisheries Service
Santa Rosa Area Office
777 Sonoma Avenue, Room 325
Santa Rosa, California 95404-6515
Phone: 707-575-6097
Fax: 707-578-3435

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What is Involved in Processing a Permit Application?
Once we receive a complete permit application, it is subject to a 30-day public comment period.
The 30-day public comment period begins when a "notice of receipt" is published in the Federal
Register (required by regulations). We may also distribute the application for review by
scientific and technical experts, resource managers, and/or other Permit Holders. After the 30day public comment period, we will forward a summary of the comments for the applicant to
address. The applicant must submit a written response.
We must then conduct an ESA section 7 consultation on the proposed activity. This, in turn,
results in a biological opinion on the activity. To issue a section 10(a)(1)(A) permit for any
activity, NMFS' biological opinion must conclude that the proposed activity is not likely to
jeopardize the continued existence of any ESA-listed species nor destroy nor adversely modify
any species’ designated critical habitat.
In addition, we may be required to conduct the following consultations on the potential effects of
the activity proposed in the application: (1) Consultation with U.S. Fish and Wildlife Service
regarding potential effects on species under their jurisdiction, (2) consultation between NMFS’
Protected Resources Division and NMFS’ Habitat Conservation Division regarding any activities
taking place in Essential Fish Habitat (EFH), and (3) consultation with the National Ocean
Service if the action takes place in a National Marine Sanctuary. Any issues that arise during
these consultations may delay the permit process.
Finally, we may be required to conduct an analysis under the National Environmental Policy Act
(NEPA) if a proposed activity is one designed to enhance the propagation and/or survival of an
ESA-listed species (e.g., hatchery supplementation programs or fish salvage operations). That
analysis usually consists of an Environmental Assessment (EA) on the action of issuing a section
10(a)(1)(A) permit with conditions. In general, scientific research permits are categorically
excluded from the need to conduct an analysis under NEPA.
After we receive responses from the applicant to the public comments and complete a biological
opinion (and any other required consultations), we will decide whether or not to issue the permit.
In order to issue such a permit, we must find that it: (1) Was applied for in good faith, (2) if
granted and exercised will not operate to the disadvantage of listed species subject to the permit,
and (3) will be consistent with the purposes and policies set forth in the ESA. We will then
notify the applicant of the decision and publish a notice about the decision in the Federal
Register (required by regulations).
How Do I Modify an Existing Permit?
A request to modify an existing permit should address all sections of these instructions relevant
to the requested change and include a detailed description and justification of the proposed
changes. Modification requests involving an increased number of animals, increased risk to the
species, additional listed species, or significant changes in the nature or location of activities may
be subject to a 30-day public review period and re-consultation on the effects of issuing the
modified permit.

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Paperwork Reduction Act and Confidentiality Information
An applicant must submit the information requested in the following instructions to obtain an
ESA section 10(a)(1)(A) permit. We will use that information to process the permit request in
accordance with the ESA. The information provided is not confidential and is subject to public
review and comment.
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 (Office of Management and Budget) OMB Control Number. In addition,
persons are not required to retain records for more than three years unless those records are
health, medical, government contract, grant-in-aid, or tax records.
NMFS estimates that the average time to compile an application in accordance with these
instructions is 20 hours. This includes the time needed to review instructions, search existing
data sources, gather and maintain the data needed, and complete and review the application. For
annual permit reports, NMFS estimates average response time at 10 hours per report. You may
send comments regarding these estimates or any other aspect of this information collection,
including suggestions for reducing this burden, to the addresses under Where Do I Send the
Application?

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Complete all fields in the following tables. After you have completed
the tables, read the certification statement and sign and date the
certification page. If you require more than what is provided, please
make copies of the table and attach them to the application.
Instructions are found at the end of the document.
A. Project Contacts Information
Applicant/Holder
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned

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Responsible Party
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
Principal Investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
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Primary Contact
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
Co-investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
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Co-investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
Co-investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
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Co-investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
Co-investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned
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Co-investigator
First Name
Last Name
Title:
Organization:
Division:
Mailing Address:
City:
State:
Zip:
Primary Phone:
Secondary Phone:
Title:
Email:
Degrees Earned

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B. Project Information

Project Title:

Application Date

Project Status:

Previous Federal:

Permit Requested:

Where will activities
occur?

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Research
Timeframe

Start:
End:

Sampling Season/
Project Duration:

Abstract:

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C. Project Description

Project Purpose:

Project Description:

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D. Supplemental Information

Status of the
Species:

Methods:

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Lethal Take:

Anticipated Effects
on Animals:

Measures to
Minimize Effects to
Listed Species:

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Resources Needed to
Accomplish
Objectives:

Disposition of
Tissues:

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E. Federal Information
Federal Agency
Type

Number and Title
Date Signed
Expiration Date

Listing Units/Stocks covered

Comments

Federal Agency
Type

Number and Title
Date Signed
Expiration Date

Listing Units/Stocks covered

Comments

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Federal Agency
Type

Number and Title
Date Signed
Expiration Date

Listing Units/Stocks covered

Comments

Federal Agency
Type

Number and Title
Date Signed
Expiration Date

Listing Units/Stocks covered

Comments

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F. Location/Take Information
Location #1 Description
State/Territory:

Basin (4th Field HUC):

Estuary:

Marine Zone:

Ocean Area:
Waterbody:
Begin Mile:
End Mile:
Township, Range, Section,
Latitude, Longitude, UTM
Northing, and UTM
Easting:

Location Description:

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Take Table Location #1
SPECIES

LISTING UNIT/STOCK

PRODUCTION/ORIGIN

LIFESTAGE

SEX

EXPECTED
TAKE

INDIRECT
MORTALITY

21

TAKE ACTION

OBSERVE/COLLECT
METHOD

PROCEDURES

RUN

BEGIN
DATE

END
DATE

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Location #2 Description
State/Territory:

Basin (4th Field HUC):

Estuary:

Marine Zone:

Ocean Area:
Waterbody:
Begin Mile:
End Mile:
Township, Range, Section,
Latitude, Longitude, UTM
Northing, and UTM
Easting:

Location Description:

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Take Table Location #2
SPECIES

LISTING UNIT/STOCK

PRODUCTION/ORIGIN

LIFESTAGE

SEX

EXPECTED
TAKE

INDIRECT
MORTALITY

23

TAKE ACTION

OBSERVE/COLLECT
METHOD

PROCEDURES

RUN

BEGIN
DATE

END
DATE

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Location #3 Description
State/Territory:

Basin (4th Field HUC):

Estuary:

Marine Zone:

Ocean Area:
Waterbody:
Begin Mile:
End Mile:
Township, Range, Section,
Latitude, Longitude, UTM
Northing, and UTM
Easting:

Location Description:

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Take Table Location #3
SPECIES

LISTING UNIT/STOCK

PRODUCTION/ORIGIN

LIFESTAGE

SEX

EXPECTED
TAKE

INDIRECT
MORTALITY

25

TAKE ACTION

OBSERVE/COLLECT
METHOD

PROCEDURES

RUN

BEGIN
DATE

END
DATE

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G. National Environmental Policy Act (NEPA) Considerations
Question #

Answer

Experimental or
Controversial
Techniques?

Infectious Agents
or Pathogens

Unique
Geographic
Areas

National Register
of Historic Places

Transport of
Materials

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H. Certification
The applicant or responsible party must read the following paragraph and provide a signature,
name, position title, and date.
"I hereby certify that the foregoing information is complete, true and correct to
the best of my knowledge and belief. I understand this information is submitted
for the purpose of obtaining a permit under the Endangered Species Act of 1973
(ESA) and regulations promulgated thereunder, and that any false statement may
subject me to the criminal penalties of 18 U.S.C. 1001, or to penalties under the
ESA."

_______________________________________
Signature

_____________________
Date

_______________________________________
Name and Position Title (print)

Length of Time and Cost to Prepare Application (Optional): The public burden of these
application instructions is evaluated periodically by the Office of Management and Budget under
the Paperwork Reduction Act. Your response will help improve the accuracy of the estimates
given for evaluation. You may send comments regarding this estimate or any other aspect of this
information collection, including suggestions for reducing this burden, to the address under
Where Do I Send the Application?
1. Please estimate the length of time, in hours, it took to compile this application.
2. Please estimate the cost, in $US, of compiling this application, excluding the labor
hours identified in 1. above. This estimate should include: cost of paper, printing,
mailing, photocopying, etc.

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Application Instructions 
A. Contacts Information:
Complete all fields using the instructions below. If you require more than what is provided,
please make copies of the table and attach them to the application.
Applicant/Permit Holder – The person, institution, or agency that is ultimately responsible
for all activities of any individual who is operating under the authority of the permit. Where
the Permit Holder is an institution or agency, the Responsible Party is the official who has
the legal authority to bind the organization (see definition below).
Note: The Applicant becomes the Permit Holder once a permit is issued. There can be only
one Applicant/Permit Holder. Permits are not transferable from one Permit Holder to another
and the Applicant/Permit Holder cannot be changed. In many cases, the Applicant/Permit
Holder may be the same as the Principal Investigator (PI) and/or Primary Contact. All
requests related to the permit must be submitted in writing (email accepted) by the Permit
Holder or Principal Investigator. The request may come from the PI if the PI has signed the
application and permit.
Responsible Party – This role is only used if the Applicant/Permit Holder is designated as
an agency or organization. The Responsible Party is an official who has the legal authority
to bind the organization, institution, or agency that is ultimately responsible for all activities
of any individual who is operating under the authority of the permit.
Note: Where an applicant for a permit is an organization, institution, or agency rather than an
individual, the application and permit must be signed by the Responsible Party. An example
is that the Responsible Party for a National Marine Fisheries Service (NMFS) Science Center
is the Center Director. The Responsible Party can change with approval from the agency
issuing the permit.
Principal Investigator (PI) – The individual primarily responsible for the taking,
importation, exportation, and any related activities conducted under a permit issued for
scientific research or enhancement purposes. The PI must have qualifications, knowledge
and experience relevant to the type of research activities authorized by the permit.
Note: The PI must be on site during any activities conducted under the permit unless a CoInvestigator is present to act in place of the PI. There can be only one PI on a permit. The
PI may also be the Applicant/Permit Holder and Primary Contact. Because the PI supervises
the research, NMFS requires that the PI submit a CV/resume.
Co-Investigator (CI) – Individuals who are qualified and authorized to conduct or directly
supervise activities conducted under a permit issued for scientific research or enhancement
purposes without the on-site supervision of the PI.
Note: CIs assume the role and responsibility of the PI in the PI’s absence. There can be
numerous CIs designated under a single permit. The CI is authorized to work independently
in the field or lead a field crew. For example, there could be separate CIs in charge of
distinct activities/projects under a permit, or responsible for distinct geographic areas under a
permit. Because a CI can supervise research, NMFS requires that a CV/resume be provided
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for each CI (for ESA Section 10(a)(1)(A) permits and all MMPA permits). There can be
only one PI per application. If a project has multiple principals, one person must be assigned
the PI role and the others assigned CI roles.
Primary Contact – The person primarily responsible for correspondence during the permit
review process and after a permit is issued.
Note: The Primary Contact may be separate from or hold any other role on the permit
(Applicant/Permit Holder, PI, etc.). While the Primary Contact may engage in
correspondence on behalf of the Applicant/Permit Holder (such as providing minor
clarifications for information in the application, making inquiries as to the status of an
application and the application process, and submitting reports on behalf of the
Applicant/Permit Holder), any substantive changes or requests for modifications must be
submitted by the Applicant/Permit Holder or PI.
Please attach résumés for PIs and CIs, or submit them as a separate document.

B. Project Information:
Complete all fields using the instructions below. If you require more than what is provided,
please make copies of the table and attach them to the application.

Project Title: Describe the project as concisely and descriptively as possible. Include the
study’s geographic range and purpose.
For example: “Seasonal habitat selection by westslope cutthroat trout in headwater tributaries
of the John Day River.” Or “Use of restored estuarine marsh channels/habitats by juvenile
salmonids in the Siletz River Basin.”
Date of Permit Application: Date you are sending the application. If you submit
subsequent versions of the application (after you receive guidance from NMFS) update the
dates to reflect the date the updated version is sent.
Project Status: Project status indicates whether or not the project is new. If you are
requesting a renewal of an existing permit, indicate this in the “Previous Federal Permit
Section” below.
Previous Federal Permit #: If you are renewing or modifying a permit, please indicate the
previous permit number here.
Permit Requested: Indicate what type of section 10(a)(1)(A) permit you are applying for:
1.

Application for Permit for Scientific Purposes under the Endangered Species Act
of 1973. (If the proposal is for field surveys, genetics research, etc.)

2.

Application for Permit to Enhance the Propagation or Survival of Listed Species
under the Endangered Species Act of 1973. (If the proposal is for fish hatchery
operations, etc.)
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3.

Application for Permit for Scientific Purposes and to Enhance the Propagation or
Survival of Listed Species Under the Endangered Species Act of 1973. (If the
proposal is for activities that fall under both categories 1 and 2 above)

4.

Application for Modification of Existing Permit.

Where will the activities occur? Please indicate where the activities will occur: California,
Idaho, Oregon (including the Columbia River and offshore waters), Washington (including
the Columbia River and offshore waters), International waters (including Antarctica and high
seas), Foreign countries, including territorial waters of those countries
Research Timeframe: Provide the start and end dates of your activities for which you are
seeking a permit. The start date must not be prior to the date that you submit the application.
The end date should be within five years of the start date. If your research extends beyond
these dates, please provide that information under “Sampling Season/Project Duration.”
Please provide realistic dates so that permit issuance can be prioritized to ensure all
researchers receive authorization in time for their field work. For example, do not give a
start date of January 1 and an end date of December 31 if you will not be conducting an
activity throughout the entire year. However, the dates listed should allow some flexibility
for unanticipated events.
Sampling Season/Project Duration: Describe the sampling season and the duration of the
project. Your description should include the months of the year and frequency of samples. If
your research extends beyond five years or your research is a continuation of previously
authorized research, provide information here about when the research began and when you
expect it to end.
Abstract: Provide a brief summary, not more than 2,000 characters, of the proposed research
and/or enhancement project. This summary will be published in the Federal Register Notice
of Receipt for a 30-day public comment period, and therefore should be understandable to a
lay reader. The summary should include concise statements of the following information:
•
•
•
•
•
•
•

Identify the ESA listed species that would be affected by the research;
Describe the duration, purpose, goals, and location of the research;
Describe how the study would benefit the affected species;
Describe the type and manner of take (e.g., observe/harass; capture/handle/release;
capture/tag, tissues sample/release; or intentional mortality);
Describe the capture methods and gear that would be used;
Describe any samples or measurements that would be taken; and
Describe how the species will be cared for after capture (e.g., fish will be placed in an
aerated bucket).

C. Project Description:
Complete all fields using the instructions below. If you require more than what is provided,
please make copies of the table and attach them to the application.
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Project Purpose (Hypothesis/Objectives): This should be a brief description of the overall
objective of the project. Indicate if this project fulfills requirements or recommendations of
federal or state agencies. Also, if applicable, describe how this project fits into a larger series
of projects or research plan. Please include a justification for the project especially if listed
fish may be taken and an account of how the project might benefit the listed fish (if
applicable). There will be space for a more complete description of your project in the next
section.
Project Description: Please include a thorough description of your project. Include all
methods used to capture fish and describe how fish will be handled. Include details such as
sampling locations and dates. Describe any intrusive procedures such as tagging or taking
tissue samples and explain the purpose of them (e.g. fin tissue will be collected from a
portion of fish sampled for genetic analysis). A project proposal may be attached to
supplement the project description (see below). However, a brief summary of the attached
files should be included in this field.

D. Supplemental Information:
Complete all fields using the instructions below. If you require more than what is provided,
please make copies of the table and attach them to the application.
Status of Species: Describe the recent status and trends of each listed Evolutionarily
Significant Unit (ESU), Distinct Population Segment (DPS), or species proposed to be taken
(include citations where possible). NMFS already possesses information at the ESU/DPS
level (see various NMFS web sites), so there is no need to repeat it in your application. We
are seeking new data here—specifically, status and trend data on any distinct populations the
proposed action is likely to affect. Such information will help us evaluate the probable
impacts of the proposed research.
Methods: Include all methods used to capture fish and describe how fish will be handled.
Include details such as capture methods, anesthesia to be used, and sampling locations and
dates. Describe any invasive procedures such as marking, tagging or taking tissue samples
and explain the purpose of them.
Note: You may not anesthetize any fish that may be taken in a legal fishery unless you
are using a Federal Drug Administration approved anesthetic and protocols. For
information about approved anesthetics please see the Federal Joint Subcommittee on
Aquaculture’s Guide to Drug, Vaccine, and Pesticide Use in Aquaculture
(http://aquanic.org/jsa/wgqaap/drugguide/drugguide.htm ).
Lethal Take: You must provide a description of the lethal take you are requesting and why
it is important to your project. Please include an adequate justification for killing listed fish.
If you do not expect to intentionally kill any listed species, please indicate this in the methods
section above.
Anticipated Effects on Animals: Describe the effects of the research on the behavior and
physiology of the fish. Include a description of the probability of mortality.

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Measures to Minimize Effects to Listed Species: Describe what adjustments have been
made to the sampling plan to minimize impacts to listed fish (e.g., reduced sample size;
modified sampling times, locations, or methods; or non-lethal tissue collection). If your
application includes electrofishing, you must indicate in this box that you will follow the
NMFS 2000 Electrofishing Guidelines.
Resources Needed to Accomplish Objectives: Explain how your expertise, facilities, and
resources are adequate to successfully accomplish the objectives and activities stated in your
application. Include the name and address of sponsors, cooperating institutions/researchers,
or contractors, if not listed as Co-investigators on the application. If the proposed activities
will be conducted by a contractor, provide a statement that a qualified member of your staff
(include name(s) and qualifications) will supervise or observe the taking. Attach copies of
any relevant formal research proposals, contracts, or letters of agreement that would
demonstrate the financial or logistical resources available to you to conduct and complete the
proposed activities.
Disposition of Tissues: Provide a description of the disposition of any parts or samples
remaining after the research or enhancement activities are complete. If you have made
arrangements with a museum or other institutional collection to ensure that remaining tissues
will be available for scientific research or enhancement purposes, include information on
where the samples will be stored, transferred, and how/when/where they will be disposed.
Include contact information for each of researchers, laboratories, museums, and/or
institutional collections that would receive these tissue samples or specimens. If you will not
retain samples, state whether samples/dead carcasses will be returned to their capture site, or
that samples will be consumed in analysis or will be destroyed.
Public availability of product/publications: Identify the anticipated or known availability
of progress reports, publications, articles, etc. related to the project. For example, the URL
for a web site hosting annual progress reports for a multi-year project.

E. Federal Information:
Using the instructions below, Enter information about any Federal authorizations (other than
the ones you are applying for here) in the table in Appendix III. More federal information
charts are attached to this application. If you need more than are provided, please make a
copy of the chart in Appendix III and attach it to this application. Enter information about
Federal agencies who fund the work, issue permits to allow the work, cooperate with the
work, or provide any other authorizations so the research can be done.
Note: Permits may include Corps 404 permits. Authorizations may include USFWS section 6
agreements, or USFWS or NMFS section 7 consultations. Attach a copy of the authorization
if you have one, or you may be required to mail or Fax a copy if requested.
Federal Agency: Include the name of the Federal agency.
Type: Identify the type of Federal action or permit.
Number and Title: Indicate the reference number of the authorization and its title. The title
can be abbreviated if necessary.
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Date Signed: Enter the month, day and year that the authorization or activity (e.g., grant,
MOU) became effective. If the action is pending, use the comments section to describe the
expected date of completion.
Expiration Date: The date the Federal agreement expires. While not required, this is an
important field for authorizations with an expiration date.
Listing Units/Stocks covered: Identify the listing units or stocks covered by the
authorization.
Comments: Include information, as described above, for authorizations pending. This field
may also be used to provide details such as if only a portion of a project is covered by the
authorization.

F. Take/Location Information:
Record take estimates for all activities using the Take Table. You must use a separate take
table for each 4th field HUC. If you need more Take Tables you can make copies and attach
them to the application. The Take Table spreadsheet has two sections: The location
information for the associated take table located directly below; and the take table.
For each line in the take table you must include the species or species group to be taken, the
quantity of each species, method of capture, intrusive procedures, and sample dates. The
information must be specific to the location listed at the top of the page. For a list of the data
options for the take table categories please see the tables below.
i. Take Location(s)
State/Territory: Identify the state in which the take will occur.
Basin: Identify the subbasin you will be working in. A separate location entry is required for
each subbasin you will be working in. List subbasins that are at the scale of 4th field
hydrologic units (sometimes called 4th field HUCs). If you wish to see more detailed subbasin maps for the Northwest Region you can use the Streamnet Interactive Mapping tools
located at http://map.streamnet.org/. This site includes sub-basin and species distribution
maps for Oregon, Idaho, and Washington. Alternatively, you can use the search tool at
United States Environmental Protection Agencies Surf Your Watershed web page
(http://cfpub.epa.gov/surf/locate/index.cfm).
Estuary: If you will be working in the estuarine zone, include the appropriate estuarine
region. However, if your research location is the Pacific Ocean or the marine waters of the
Puget Sound, do not select a subbasin. The next item below is used for Puget Sound marine
habitats.
Marine Zone: If you will be working in the marine portion of the Puget Sound, you must
identify the marine zone(s). Contact Gary Rule for a map of the marine zones
([email protected] or 503-230-5424):

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Shoreline: If your proposed project would occur in marine waters of Oregon, you must
identify a shoreline zone.
Ocean Area: If your proposed project would occur in marine waters of Oregon, you identify
an ocean area.
Waterbody: Include the name(s) of the lake(s), river(s), or estuary(s) where you will be
conducting your research. If you wish to list the waterbodies, you may include a detailed
stream with your application. Specific stream names must be supplied when they are
available. You may also enter a subwatershed
Begin Mile: For projects that would occur within stream habitats, you may provide the
beginning river mile for your project.
End Mile: For projects that would occur within stream habitats, you may provide the ending
river mile for your project.
Township, Range, Section, Latitude, Longitude, UTM Northing, and UTM Easting: If
you have this information, you may provide it.
Location Description: You may describe any landmark or geographic reference to where the
project would be conducted. If sites have not yet been selected you can explain how they
will be selected. Specific sites must be supplied when they are available. For example, if
you provided a sub-basin name you should provide the names of the specific streams that
will be sampled.
Note: You may include attachments (i.e. maps, charts etc…) detailing specific survey
sites within a sub-basin. However, you must still complete a take estimate for every subbasin in which you will be collecting.
ii. Take Information:
You will include a separate record for each unique combination of species, production type,
life stage, take action, and capture method. For example, if you will take both artificially
propagated and naturally produced Chinook salmon, you will need at least two records. If
you will also take tissue samples from a portion of the catch, you will have four records: one
for capture, handle, and release of hatchery Chinook salmon; one for capture handle and
release of natural Chinook salmon; one for capture/mark, tag, sample tissue/release hatchery
Chinook salmon; and one for capture/mark, tag, sample tissue/release natural Chinook
salmon.
Species: The common and/or scientific name of the listed marine or anadromous fish.
NOAA Fisheries maintains a list of species on its’ web site at
https://apps.nmfs.noaa.gov/docs_cfm/species_lists.cfm. If you are unsure about the species,
you can request assistance by contacting the appropriate NMFS Office (see the section
“Where Do I Send the Application?” section above to find the NMFS Office contact
information).

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Listing Unit/Stock: Choose the listing unit/stock of the take species in your study region.
Listed populations of salmon, steelhead, and other marine fishes can be found on the
Northwest Regional Office’s web site at http://www.nwr.noaa.gov/.
Production/Origin: The categories are: naturally produced; listed hatchery with a clipped
adipose fin; listed hatchery with an intact adipose fin; and unlisted hatchery. If you will take
more than one category, you will need to enter a separate row for each one. For more
information on the listing status of hatchery fish, visit http://www.nwr.noaa.gov/ESASalmon-Listings/Salmon-Populations/Index.cfm.
Life Stage: If you will take more than one life stage (e.g., adult and juvenile) you will need
to enter a separate row for each life stage you will encounter. The options are juvenile,
smolt, adult, or spawned adult/carcass.
Sex: If your activity is targeting one sex indicate which sex is targeted. Otherwise, select
“Male and Female.”
Expected Take: Enter the number of individual animals you expect to capture, observe, etc.
(depending on the “Take Action” you selected). If you are entering take for a location
representing multiple sites in a sub-basin, the expected take should equal the total take for all
sites in that sub-basin. You are not required to estimate expected take for “Observe/Harass.”
For “Intentional (Directed) Mortality,” enter the number of individuals you will purposely
kill.
Indirect Mort: Enter the number of individual animals you expect will be unintentionally
killed as a result of your activities. If the take action is “Intentional (Directed) Mortality,”
then enter zero for the indirect mortality. When the action is intentional mortality, there are
no indirect mortalities.
Note: Acceptable Indirect Mortality rates are up to 5% of the total per species for
electrofishing and gill netting and up to 1% of the total per species for other methods. If you
expect higher indirect mortality rates you must provide justification in the “Anticipated
Effects on Animals” section of your application.
Take Action: If more than one action is proposed, you must enter them separately. For
example, if 100 fish are captured of which 50 will be fin clipped, you must request 50 fish
“Capture, Handle, Release” and 50 “Capture/Mark, Tag, Sample Tissue/Release Live
Animal.”
1. Capture/Handle/Release Fish: Select this method when fish are captured during the
activity. Fish can be examined during handling, including measuring, weighing,
sexing, checking for marks, scars, etc., and released. This category of take includes
fish shocked during boat or backpack electrofishing activities, even if the fish swim
away and are not netted.
NOTE: If you are electrofishing you must state in the Minimize Impacts section
on your application that you will follow the “NMFS 2000 Electrofishing
Guidelines.” Visit http://www.nwr.noaa.gov/ESA-Salmon-Regulations-Permits/4drules/upload/electro2000.pdf
for a copy of the guidelines.
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2. Capture/Mark, Tag, Sample Tissue/Release Live Animal: Select this method
when fish are captured and are marked, tagged, or tissue samples are taken using a
variety of techniques including fin clips, coded wire tags, passive integrated
transponders, radio tags, etc. Fish can also be examined during handling, including
measuring, weighing, sexing, checking for marks, scars, etc., and then released.
NOTE: If you select this action you must also include the Procedure(s) that will
occur.
Include one or more methods from the Procedures listed in Appendix II.
3. Collect and Transport Live Animal: Select this method when fish will be
transferred live from the point of collection to another site, usually to a facility, but
also for fish being relocated to another stream, sub-basin, etc. Do not use for fish
being moved within a stream (e.g., trap efficiencies). If you select “Collect and
Transport Live Animal” as the take action, include the following information in your
project methods section labeled Transport Info:
Mode(s) of transportation: Describe the mode of transportation. Include a description
of the vehicle used to transport animals and the name of the transportation company,
if applicable, and the qualifications of the common carrier to transport live animals.
Specify whether a contractor will do the transportation, and include any relevant
information.
Transport time: Estimate the maximum amount of time an animal may be in transport.
Qualified transport personnel: Give the name, affiliation, contact information for each
person.
Destination: If the animals will be taken to a laboratory, classroom, or aquarium,
provide details of the location. If the animals will be released in another waterbody,
provide details of the location.
Containment methods: Describe the containment system for the animals, quarantine
procedures, and effluent treatment. Description of the container (e.g., cage, tank)
used to hold the animal during transit, including the material of the container and its
dimensions. Include any special care procedures (e.g., moisture, medicines, aeration)
to be administered during transport. The final disposition of the animals Describe, for
example, whether the fish will be released, sacrificed, or deposited in a museum
collection (e.g., “Retain alive for six months, then release”; “Sacrifice for tissue
analysis.”).
4. Intentional (Directed) Mortality: These are fish that will be purposely killed (e.g.,
for otolith analysis). You must describe in the “Project Description” why you wish to
purposely kill these fish.
NOTE: For entries that are direct mortality, enter zero for the indirect mortality!
5. Observe/Harass: Select this method when no fish will be handled or captured in any
way. You do not have to estimate expected take for this activity.

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6. Observe/Sample Tissue Dead Animal: Select this method when information on
dead fish is recorded or tissues are sampled from dead fish.
Observe/Collect Method: List the method of observation or capture. You may only select
one observe/collect method per take. If you will be using various methods, you must use a
separate row for each observe/capture method. Chose from the following list:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•

CaptureMethod
Benthic Core < 10” diameter
Benthic Core > 30” diameter
Benthic Core 10-30” diameter
Crab traps or rings
Dam bypass, gatewell, orifice, etc. (only if associated with fish handling)
Electrofishing, Backpack
Electrofishing, Boat
Fish Ladder (only if associated with fish handling)
Fish Screens, e.g., at diversions (only if associated with fish handling)
Gaff
Hand and/or Dip Net
Hand held-spatula/knife
Hook and line/angler/rod and reel
Longline
Net, Cast
Net, Fyke
Net, Gill
Net, Hoop
Net, Kick
Net, Neuston
Net, Pop
Net, Tangle
Net, Tooth
Net, Trammel
Net, Zooplankton
Plankton Pump
Seine, Beach
Seine, Lampara
Seine, Purse
Shovel
Throwbox
Trap, Buckley
Trap, Light
Trap, Minnow
Net, Trap
Trap, Screw
Trawl, Beam
Trawl, Bottom
Trawl, Midwater
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•
•
•
•
•
•
•

Expiration Date: 02/28/2009

Trawl, Nordic Surface
Trawl, Otter
Weir (only if associated with fish handling)
Seine, Boat
Fish Pot
Trap, Incline Plane
Trap, Not listed here

Procedure: If you intend to “Capture/Mark, Tag, Sample Tissue/Release Live Fish” you are
required to select at least one intrusive method. List all intrusive methods you intend to use
for each associated take action. Chose from the following list:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•

IntrusiveMethod
Anesthetize
Dye Injection (tattoo, photonic)
Finclip
Freeze Brand
Maxillary Clip
Paint, Stain or Dye Immersion
Punch (opercle, caudal, etc.)
Stomach pump (non-lethal)
Tag, Acoustic or Sonic
Tag, Balloon
Tag, Coded-Wire
Tag, Elastomer
Tag, Floy
Tag, PIT
Tag, Radio (External)
Tag, Radio (Internal)
Tissue sample (other internal tissues)
Tissue Sample Fin or Opercle
Tissue Sample Otolith
Tissue Sample Scale

Run: Select the run timing for each listing stock/unit. Chose from the following list:
•
•
•
•
•
•
•
•
•
•
•
•

Spring
Summer
Spring/Summer
Fall
Upriver Bright Fall
Winter
Tule Fall
Odd Year
Even Year
Mixed
N/A
Unknown
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Begin/End Date: These dates should reflect the timing of the associated take activity for
each line.

G. National Environmental Policy Act (NEPA) Considerations:
Please provide a detailed response to each question; a simple "yes" or "no" is not
sufficient. Your responses to the questions below will be used, along with the
information you have provided on the types of activities proposed and their effects, in
determining the potential impacts your research may have on the environment.
1. Will your activities involve equipment (e.g., scientific instruments) or techniques that
are new or may be considered experimental or controversial? If yes, are they likely to
be adopted by other researchers in the future?
2. Do your activities involve collecting, handling, or transporting potentially infectious
agents or pathogens (e.g., biological specimens such as blood)? Do your activities
involve using or transporting hazardous substances (e.g., toxic chemicals)? If yes,
provide a description of protocols you will use to ensure humans are not infected or
injured.
3. Do any of your activities occur in or near unique geographic areas such as state or
National Marine Sanctuaries, Marine Protected Areas, Parks or Wilderness Areas,
Wildlife Refuges, Wild and Scenic Rivers, designated Critical Habitat for endangered
or threatened species, Essential Fish Habitat, etc.? If yes, would any aspect of your
activities impact the physical environment, such as by direct alteration of substrate
(e.g., by bottom trawling, net setting, anchoring vessels or buoys, erecting blinds or
other structures, disrupting nesting bird habitat)?
4. Could your work affect sites listed in or eligible for listing in the National Register of
Historic Places? Could your work cause loss or destruction of scientific, cultural, or
historic resources (e.g., archeological resources)? If yes, list the sites and explain
how they might be affected or why they would not be affected.
5. Could any of your activities, intentionally or not, involve the transport any materials,
biological or otherwise, from one area to another (e.g., transporting animals or
tissues, discharging ballast water, working in sensitive remote areas)? If yes, explain
the types of activities. Describe all measures you would take to prevent the possible
introduction or spread of nonindigenous or invasive species (including plants,
animals, microbes, or other biological agents).

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