The use of protected areas as a fishery management tool has been suggested as a hedge against management failures and variation in harvests. A stochastic bioeconomic model of a two-species fishery will be used to test the performance of protected areas as a management tool in a fishery with heterogenous environments. Protected areas are analysed under density-dependent and sink-source dispersal relationships between environments within the fishery. Differing levels of management control over fishery resource extraction are analysed. The model is applied to Manning Bioregion in NSW. The focus of the study is placed on the biological and institutional characteristics that yield benefits to the fishery.