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The fishing industry of the western and central regions of the coastal Gulf of Alaska (CGoA) directly employs over 17,000 people and processes fish with a wholesale value of US$618 million annually. Pacific halibut (Hippoglossus stenolepis) are a valued groundfish species because of the high quality of their flesh. In contrast, arrowtooth flounder (Atheresthes stomias) are much more abundant but of low value because their flesh degrades upon heating. Both are high trophic level predators but play different roles in the ecosystem because of differences in abundance and diet. Using an end-to-end ecosystem model, we evaluate the impact of alternate levels of fishing effort and large-scale changes in oceanographic conditions upon both species, the ecosystem, and the fishing economy. Reduction of longline efforts to reduce Pacific halibut mortality led to reduction in total value of all CGoA landings but increase in value landed by sport fisheries, trawl fleets, and fish pot vessels as they exploit a greater share of available halibut, sablefish, and Pacific cod. Increased trawl effort to raise arrowtooth flounder mortality led to increase in total value of all landings but large reductions in value landed by longline, jig, fish pot, and sport fleets with greater competition for available Pacific cod, halibut, and sablefish. Oceanographic conditions that enhance pelagic food chains at the expense of benthic food chains negatively impact groundfish in general, though Pacific halibut and arrowtooth flounder are resilient to these effects because of the high importance of pelagic fish in their diets.