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. The model is applied to Manning Bioregion in NSW. Protected area performance as a tool for fisheries will be analysed given the existing management arrangement. The focus of the study is placed on the biological and economic characteristics that yield benefits to the fishery.