What We Do

Scientists at the Alaska Fisheries Science Center's Auke Bay Laboratories study commercially important fish species such as rockfish, sablefish, and salmon. They conduct research to better understand where fish live during each stage of life and pinpoint what makes them unique, down to their DNA. They also examine marine ecosystems that are essential fish habitats, focusing on ocean processes and chemistry, and food web interactions that impact fish survival.

Our goal is to estimate how many fish are in Alaska’s waters through stock assessments. We also want to learn the overall health of fish species, the habitats they utilize, and the ecosystem upon which they depend. We do this through research surveys, laboratory experiments, and by updating mathematical models to gain the best information about Alaska’s commercial fish. The data biologists collect is given to the North Pacific Fishery Management Council, Alaska Regional Office, fishing industries, state and federal regulators, and international groups. These groups make decisions on how much fish can be sustainably caught.

Marine Ecology and Stock Assessment

The Marine Ecology and Stock Assessment Program has three primary functions. We 1) conduct annual stock assessments to manage the fisheries resources in Alaska waters, 2) conduct annual surveys to assess the status of these resources, and 3) perform ecological research process studies to inform stock assessments and  advance ecosystem-based fisheries management.

Specifically, we produce annual stock assessment and fishery evaluation reports for sablefish, rockfish, and sharks in Alaska. We use a variety of fish population models to integrate fishery catch, survey data, biological observations, and theoretical considerations to recommend annual fish quotas. We conduct an annual longline survey and tagging studies to provide information for the stock assessments for Pacific cod, skates, Pacific halibut and other flatfish. Field and laboratory studies provide important information on different aspects of fish life history such as recruitment (i.e., when a fish is large enough to be caught by a commercial fishery), movement, growth, maturity, and natural mortality. We integrate this ecosystem process research into our stock assessments to support ecosystem-based fisheries management. Our program also conducts research on essential fish habitat, benthic habitats, and cold water corals and the effects of fishing on these sensitive ecosystem components. In our work, we often collaborate with other scientists, both within NOAA and with external partners, and with fisheries managers, stakeholders, and the general public. The Salmon Ocean Ecology and Bycatch Assessment Program provides an annual pink salmon forecast.

Recruitment, Energetics, and Coastal Assessment

The Recruitment, Energetics, and Coastal Assessment program develops and monitors indicators of ecosystem status and energy flow through different trophic levels in the marine food chain. Our analytical products can be used with survey data to assess the response of juvenile year classes (young age groups of fish) of fish to changing environmental conditions and to identify essential fish habitat. Young fish survival is key to understanding future fish population productivity. Our goal is to provide indicators of fish population productivity and protected resources population health (e.g., humpback whales) for resource managers use.

We conduct fully-integrated studies from sample collection to modeled results, and peer reviewed publications. We conduct field projects in nearshore waters and laboratory experiments designed to understand how fish respond to environmental change. Our state-of-the-art chemistry lab is the Center's largest analytical laboratory. We perform broad-spectrum analyses on fish health and condition to better understand food webs and processes of ecosystem change and recruitment variability in Alaska’s nearshore habitats. These analyses include indices for fish growth (RNA/DNA), nutritional status (proximate analysis, thiamine levels, bioenergetic measurements (diet, calorimetry) and prey resource identification (genomics, fatty acid analysis and compound specific stable isotope analysis). We acheive our work through extensive collaborations within NOAA and with external partnerships.

Ecosystem Monitoring & Assessment

Through research surveys and other studies, Ecosystem Monitoring and Assessment Program scientists collect information from Alaska’s Large Marine Ecosystems including the Arctic, Eastern Bering Sea, and Gulf of Alaska. We collect data and information on temperature, salinity, oxygen, nutrients, phytoplankton (tiny plants), zooplankton (marine bugs), jellyfish, and fish. We use this information to understand what causes changes in the growth, fitness, and survival of fish including: walleye pollock, Pacific cod, Arctic cod, saffron cod, sablefish, rockfishes, salmon (i.e., Chinook, chum, sockeye, pink, and coho),, arrowtooth flounder, and forage fishes such as Pacific herring, capelin, sandlance. Our research results are used to help develop Alaska marine ecosystem status reports and provide scientific advice to manage and protect marine resources and human communities.

Chinook and chum salmon are incidentally caught in federally managed fisheries in the Gulf of Alaska and Bering Sea. We combine data from fishery and non-fishery sources to study targeted catch rates, bycatch rates and how bycatch varies by area and different times of year. Bering Sea and Gulf of Alaska surveys focus on early marine ecology of salmon. Field stations (Little Port Walter and Auke Creek) conduct research on factors that affect marine migration, survival and shifts in age and physical characteristics of Chinook and other salmon. Samples of Chinook and chum salmon from the commercial fishing fleet and from tagged fish caught in salmon and non-salmon fisheries are used to determine the age and stock origin (i.e., the natal streams). Information from these data sets provide a better understanding of the impact of bycatch on specific stocks of salmon.


The Genetics Program provides data on where fish come from. This information is required in regional, national, and international agreements and treaties to manage Pacific salmon, groundfish, and forage fish species.  DNA, a natural mark, can be used to identify both species and stocks of fish. Identifying what species or stocks of fish are caught, what habitats they use, and where they migrate is important information for fishery management.  

In our current research, we are trying to determine the origin of Chinook and chum salmon stocks incidentally caught (bycatch) in the Bering Sea and Gulf of Alaska groundfish fisheries. We are also working to identify point of origin for sockeye salmon harvested in Pacific Salmon Treaty fisheries in Southeast Alaska, and juvenile salmon collected in the eastern Bering Sea, off the Yukon River during our summer/fall surveys. Other genetic research is focused on the stock structure of herring, Arctic cod, capelin, and the identification of new forage fish species.

Our Leadership


Advanced Technologies

Our scientists use a varitey of innovative technologies as they collect data and information to better understand the science behind healthy ecosystems and marine life.

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