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ABSTRACT. The use of marine protected areas (MPAs) as a basic management tool to limit exploitation rates in marine fisheries has been widely suggested. Models are important in predicting the consequences of management decisions and the design of monitoring programs in terms of policy goals. However, few tools are available that consider both multiple fleets and ecosystem scale dynamics. We use a new applied game theory tool, Ecoseed, that operates within a temporally and spatially explicit biomass dynamics model, Ecopath with Ecosim, to evaluate the efficacy of marine protected areas in the North Sea in both ecological and economic terms. The Ecoseed model builds MPAs based on the change in values of predicted economic rents of fisheries and the existence value of biomass pools in the ecosystem. We consider the market values of four fisheries operating in the North Sea: a trawl fishery, a gill net fishery, a seine fishery, and an industrial (reduction) fishery. We apply existence values, scaled such that their aggregate is similar to the total fishery value, to six biomass pools of concern: juvenile cod, haddock, whiting, saithe, seals, and the collective pool ‘Other predators’ that include marine mammals. Four policy options were considered: to maximize the rent only; to maximize the existence values only; to maximize the sum of the rent and existence values; and, finally, to maximize the sum of the rent and the existence values, but excluding only the trawl fleet from the MPA. The Ecoseed model suggests that policy goals that do not include ecological considerations can negatively impact the rents obtained by the different fishing sectors. The existence values will also be negatively impacted unless the MPA is very large. The Ecoseed model also suggests that policy goals based solely on existence values will negatively impact most fisheries. Under policy options that included ecological considerations, maximum benefits were derived from an MPA that covered 25–40% of the North Sea, placed along the southern and eastern coasts. Finally, the Ecoseed model suggests that an exclusion of the trawl fishery only from the MPA can provide small-to-substantial positive impacts to most species and fleets; this relative impact depends on level of interaction between the trawl fleet and the other fleets target species (e.g., through bycatch).