Marine protected areas (MPAs) are increasingly employed worldwide to manage and conserve marine ecosystem services such as fisheries, coastal protection, habitat restoration, biodiversity conservation and tourism. They are frequently used as a place-based approach with the aim of conserving fishery resources by restricting fishing to specific zones. MPAs are particularly useful for managing species that are not highly migratory since these species’ habitats can be restricted to ranges within zoning boundaries. For example, benthic communities and many invertebrate fisheries can be managed by the use of MPAs because their habitat ranges can be delineated and zoned for protection or exploitation. In this work, I have researched ecological interactions in the benthic community of MPAs and evaluated governance strategies used to promote compliance with MPA regulations. Enforcement of MPAs remains one of the key factors in ensuring sustainable resource use for some fisheries, though enforcement mechanisms leading to successful outcomes remain poorly understood worldwide. As a result, it is necessary to consider how different governance strategies used to encourage compliance with MPA regulations may best sustain fishery resources. In chapter one, I have analyzed different strategies used to promote compliance with regulations on ecological indicators of condition in the Greater Caribbean region. I found that the use of both penalties and incentives to promote compliance may help form successful governance strategies. I also have examined ecological relationships affected by the presence of MPAs. In chapter two I evaluate the distribution of an invasive tunicate, its interaction with the Atlantic sea scallop and the impact of the protected area as compared to open areas on this interaction. In chapter three I evaluate how the invasive tunicate interacts with other species of the invertebrate community and how these interactions are altered by the protected area and the presence of fishing. This work enhances our understanding of marine management, though an analysis of MPA governance and ecological interactions shaped by MPAs. Understanding both the governance and ecological aspects of MPAs provides a holistic framework for understanding their utility for marine conservation and management.