This article compares and contrasts the concepts of fisheries refugia and marine protected areas. Specifically, the potential benefits to fisheries associated with the use of both management tools in the Southeast Asian region are also evaluated. The paper argues that in the case of the MPAs, the objectives are often broadly focused at the ecosystem level rather than on species of importance to local fisheries, while the sites are selected on the basis of biodiversity criteria rather than on their significance to life cycle of the species concerned. Similarly, the focus on protection, rather than on sustainable use has made the MPAs generally less acceptable than refugia at the level of the primary stakeholders (fisherfolk and local government officers). In the Southeast Asian region, since the focus of fisheries refugia is on the benefits to fisheries rather than the benefits to biological diversity, this has resulted in a wide acceptance of establishing such areas.