Beginning January 1, 2000, all vessels and processors wishing to participate in the non-CDQ Bering Sea and Aleutian Islands (BSAI) pollock fishery are required to have valid American Fisheries Act (AFA) permits on board the vessel or at the processing plant. AFA permits are required even for vessels and processors specifically named in the AFA, and are required in addition to any other Federal or State permits. AFA permits also may limit the take of non-pollock groundfish, crab, and prohibited species as governed by AFA "sideboard" provisions.

Management of the Alaska halibut fishery is based on an international agreement between Canada and the United States and is given effect by the Northern Pacific Halibut Act of 1982. Before fishing under the subsistence halibut regulations, fishermen must obtain a Subsistence Halibut Registration Certificate (SHARC). Special permits for community harvest, ceremonial, and educational purposes also are available to qualified Alaska communities and Alaska Native Tribes. Permit holders must comply with SHARC registration and reporting processes.

Under the IFQ Halibut/Sablefish Permit Program and CDQ Halibut Permit Program permits are issued for harvesting and receiving/processing halibut, and non-trawl sablefish. For IFQ Halibut/Sablefish Permits, owners of vessels with specific historical participation in non-trawl halibut and sablfish fisheries were issued Quota Share (QS). Quota share was initially issued to persons who owned or leased vessels that made legal commercial fixed-gear landings of Pacific halibut or sablefish during 1988-1990 off Alaska. QS is transferable to other initial issuees or to those who have become transferable eligible on NMFS' approval of an Application for Transfer Eligibility Certificate. Once issued to a person (at no charge), QS is held by that person until it is transferred, suspended, or revoked. QS permits are authorized at 50 CFR Part 679.4(d). Quota Share holders are entitled to a proportional share of the annual Total Allowable Catch allocated to the IFQ Program. An IFQ permit authorizes participation in fixed-gear harvests of Pacific halibut off Alaska, and most sablefish fisheries off Alaska. The permits are not specific to vessels. Permits are issued annually, at no charge, to persons holding fishable Pacific halibut and sablefish Quota Share (QS); or to those who are recipients of IFQ-only transfers from QS holders. Authorized pounds for annual IFQ permits are determined by the number of QS units held, the total number of QS units in the "pool" for a species and area, and the total amount of halibut or sablefish allocated for IFQ fisheries in a particular year. IFQ permits are authorized at 50 CFR Part 679.4(d). The Western Alaska Community Development Quota (CDQ) Program allocates a percentage of all Bering Sea and Aleutian Islands quotas for groundfish, prohibited species, halibut, and crab to eligible communities. A CDQ permit is required to harvest CDQ halibut. Permits are issued annually and without charge to CDQ groups with approved CDQ plans and directed fishing allocations of halibut.

The Federal Fisheries Permit (FFP) is required for vessels of the United States which are used to fish for groundfish in the Gulf of Alaska or Bering Sea and Aleutian Islands. This permit is also required for vessels used to fish for any non-groundfish species and that are required to retain any bycatch of groundfish under 50 CFR Part 679. Non-groundfish species includes but is not limited to halibut, crab, salmon, scallops, and herring. "Fishing" is a broad term and includes, for example: harvesting, processing, tendering, support, etc. These are non-transferable, three year permits, issued on request and without charge to vessel owners. The Federal Processor Permit (FPP) is required for stationary floating processors (processing vessels that operate solely within Alaska State waters). The permit also is required for shoreside processors that receive and/or process groundfish harvested from Federal waters (or from any Federally-permitted vessels). FPPs are non-transferable, three year permits, issued to owners on request and without charge.

As of January 1, 2000 a Federal License Limitation Program (LLP) license is required for vessels participating in directed fishing for LLP groundfish species in the Gulf of Alaska (GOA) or Bering Sea Aleutian Islands (BSAI), or fishing in any BSAI LLP crab fisheries. A vessel must be named on an original LLP license that is onboard the vessel. Exceptions are explained below. The LLP is authorized in Federal regulations at 50 CFR 679.4(k), definitions relevant to the program are at 679.2, and prohibitions are at 679.7. The LLP license requirement is in addition to all other permits or licenses required by federal regulations. The LLP is a Federal program and LLP licenses are not required for participation in fisheries that occur in the waters of the State of Alaska. There are four exceptions to the LLP license requirement: 1. vessels that do not exceed 26 feet in Length Overall (LOA) in the GOA; 2. vessels that do not exceed 32 feet LOA in the BSAI; 3. vessels that do not exceed 60 feet LOA and that are using jig gear (but no more than 5 jig machines, one line per machine, and 15 hooks per line) are exempt from the LLP requirements in the BSAI; and, 4. certain vessels constructed for, and used exclusively in, Community Development Quota fisheries.

The North Pacific Fishery Management Council adopted the Central Gulf of Alaska Rockfish Program (Rockfish Program) on June 14, 2010, to replace the expiring Pilot Program. The Rockfish Program became effective in 2011 and fishing under it began in 2012. The rockfish fisheries are conducted in Federal waters near Kodiak, Alaska, by trawl and longline vessels. The Rockfish Program allocates harvest privileges to holders of License Limitation Program (LLP) groundfish licenses with a history of Central GOA rockfish legal landings in either 2000 through 2006, or the entry level trawl fishery in 2007, 2008, or 2009. The Rockfish Program assigns quota share (QS) to LLP licenses for rockfish primary and secondary species based on legal landings associated with that LLP. Primary rockfish species are northern rockfish, Pacific ocean perch, and pelagic shelf rockfish. Secondary rockfish species are Pacific cod, rougheye rockfish, shortraker rockfish, sablefish, and thornyhead rockfish. Each year, an LLP license holder assigns the LLP license with rockfish QS to a rockfish cooperative. Each rockfish cooperative receives an annual cooperative fishing quota (CQ), which is an amount of primary and secondary rockfish species the cooperative is able to harvest in that fishing year. Halibut Prohibited Species Catch (PSC) is also allocated to participants based on historic halibut mortality rates in the primary rockfish species fisheries. Shore-based processors receiving rockfish CQ must be located within the boundaries of the City of Kodiak. The rockfish cooperative fishing season is authorized May 1 through November 15 of each year. An entry level fishery starts January 1 of each year for harvesters who are directed fishing for rockfish primary species using longline gear only. Catcher/processor LLP license holders may opt-out of the Rockfish Program but are subject to certain sideboard limitations, which prevent rockfish eligible harvesters from increasing their participation in fisheries other than the Central GOA rockfish fisheries.

NMFS is mandated by the Marine Mammal Protection Act (MMPA) to measure and report on the effects of commercial fisheries on marine mammal stocks. One of the ways NMFS gathers this information is through the Marine Mammal Observer Program. The program In Alaska, collects information on marine mammal interactions with commercial fisheries. This information is incorporated in assessments of the general status of marine mammal populations in Alaska.

A federal Scallop License Limitation Program (SLLP) license is required onboard any vessel deployed in scallop fisheries in Federal waters off Alaska (except for some diving operations). The SLLP is intended to limit the number of participants and reduce fishing capacity in the scallop fishery off Alaska. Regulations implementing the program were published in the Federal Register at 65 FR 78110 (December 14, 2000) as Amendment 4 to the Fishery Management Plan for the scallop fishery off Alaska and can be found at 50 CFR Part 679.4. Federal SLLP licenses are issued by the National Marine Fisheries Service, Restricted Access Management (RAM) Program. The application period for SLLP licenses closed February 12, 2001.

The Western Alaska Community Development Quota (CDQ) Program allocates a percentage of all Bering Sea and Aleutian Islands quotas for groundfish, prohibited species, halibut, and crab to eligible communities. The purpose of the CDQ Program is to provide the means for starting or supporting commercial fisheries business activities that will result in an ongoing, regionally based, fisheries-related economy in Western Alaska. This was the legacy system for managing CDQ Groundfish from 1991-2007. After 2008, CDQ groundfish was incorporated into the Catch Accounting System.

This limited access system limits the number of charter vessels that may participate in the guided sport fishery for halibut in area 2C and 3A. NMFS issues a charter halibut permit to a licensed charter fishing business owner based on his or her past participation in the charter halibut fishery and to a Community Quota Entity representing specific rural communities. All charter halibut permit holders are subject to limits on the number of permits they may hold and on the number of charter vessel anglers who may catch and retain halibut on permitted charter vessels. Permits will be issues as transferable or non-transferable and will have an area endorsement.