Marine protected areas have been advocated as a useful tool in fisheries management. However, as protected areas they are a ‘blunt’ tool to manage fishery operations; in the sense that they do not alter the incentives of individual fishers, the outcomes from protected area creation are likely to be dependent on other management mechanisms which alter incentives. Implementing protected area management of fisheries has also been viewed as beneficial in the sense that they provide a low cost management tool. In this paper, the optimal fishery management structure, in light of transaction costs, and which integrates protected areas and effort controls as a mechanism used to control the extraction of fishery resources, is explored. The policy implications of the results are also discussed.