Before the mid-1990s, Apo Island, Philippines, was often described as one of the world’s best examples of community-based marine management. This paper studies the less-documented transition of the island during the late 1990s from community-based management to centralized national state management. The Philippines was the site of some of the earliest MPAs and it now boasts well over 300, which constitute the country’s primary tool for coastal resource management. Two formats of MPA exist in the Philippines: first is the community-based ‘sanctuary’, allowing local stakeholders to manage their own resources, empowered by the Local Government Code of 1991. The second MPA format is the centralized national model, which is a prescriptive top-down method of ensuring a ‘protected land and seascape’. Extensive interviewing of islanders has revealed deep misgivings about the centralized Regime — the Protected Area Management Board (PAMB). PAMB’s aim of implementing the National Integrated Protected Areas Systems (NIPAS) Act was initially looked upon favourably by islanders, but it has lost that support because of its exclusion of stakeholders from management and its poor Institutional performance. The paper’s conclusion is that the implementation of the NIPAS Act Highlights the limitations of top-down management, and that there is a need to restore an element of local stakeholder participation in the governance of Apo’s marine protected area (MPA). A system of co-management between community and national state actors is essential to ensure the long-term sustainability of Apo’s marine resources.