This paper discusses the status, direction and management issues in the marine protected areas (MPAs) of the Bohol (Mindanao) Sea, Philippines. The MPAs in the study area have increased through the years. Many of them were established and managed by the local government units (LGUs) in collaboration with national government agencies (NGAs), academic institutions, people’s and non-governmental organizations (NGOs). Several management issues and problems were cited by the MPA managers such as insuffi cient funds and facilities, lack of support from NGAs/NGOs and lack of education among the people. Nevertheless, lessons for sustainability can be learned from the experience of some wellmanaged MPAs in the Bohol Sea. These include strong support from the political leadership, community participation and networking among the concerned sectors. Although the best practices are being followed in a number of MPAs in the Bohol Sea, success is still fragmented. The MPAs are currently managed independently although there are ongoing initiatives to network their efforts. However, it can be observed that, as a management tool, MPAs are gaining popularity and support, not only among the fisherfolk but also among local communities and LGUs in the Bohol Sea area.