A review of a major community-based marine protected area programme (CB-MPA) in an Indonesian island archipelago is the point of departure for this article. Despite a well-designed institutional structure to facilitate local participation, local knowledge about the CB-MPA is found to be low and resource access and influence on decision-making in the programme is negligible for the majority of islanders. At the same time, most of those who know about the programme consider it as pertaining to the public authority only. These findings stand in contrast to evidence on non-formal ways of protecting and managing marine areas in the same geographical area but outside the formal MPA institutiona framework. In particular, the article identifies a number of emergent rules-in-use in marine management, which operate parallel to legally established MPAs. It is argued that emergent forms of marine area protection such as non-formal self-organising island exclusion zones (IEZ) offer as yet mostly unused potentials for formal MPA development, particularly in those coastal and marine area without traditional forms of marine and coastal management.