Island nations and islands in Oceania and the Asia Pacific rely heavily on coastal and marine ecosystem services. Systems such as coral reefs, seagrass and mangroves are intrinsically important, vital to many people's livelihoods, and in many cases intertwined with cultural systems. Some, such as the reefs of the Coral Triangle, are seriously threatened by fishing pressures, including destructive fishing practices, pollution and environmental change. Governments, and concerned coastal communities, each try to work to protect or manage the exploitation of important ecosystems, yet apart from the limited cases with endorsed systems of co-management or community based management, communities and governments can find themselves working separately and not necessarily in harmony. A participatory diagnosis on the island of Selayar, Eastern Indonesia, highlights opportunities for communities and government to improvement alignment of their efforts towards sustainable management of marine ecosystems. The findings from this study can inform strategies in Oceania and elsewhere in the Asia Pacific towards improved management of marine and coastal ecosystems, from the standpoints of communities, government and civil-society actors. We highlight issues of policy alignment between communities and government; aligning customary and science-based knowledge; and navigating inter-community conflict.