Many developing countries experience habitat degradation and unsustainable natural resource exploitation, with biodiversity and habitat conservation efforts often impeded by political instability and limited funding. Challenges in previous conservation efforts coupled with the current rate of marine habitat degradation and species declines warrant consideration of an innovative conservation approach. Co-management of protected areas addresses biological, cultural, economic, and political concerns and empowers communities through collaboration and integration in conservation efforts. It provides flexibility for adaptive practices to address underlying socioeconomic factors affecting conservation efforts and may compensate for limited or missing scientific data. The ecosystems of the Comoros Islands in the West Indian Ocean, a biodiversity hotspot with high endemism and diverse tropical marine habitats, are adversely affected by existing ecological, socioeconomic, and political conditions. The Comoros example also illustrates that co-management is not immune to social issues, inadequate government law enforcement, or political instability and is an incomplete substitute for sound science. Lessons learned are applicable elsewhere and offer a template for effective scientific research and monitoring, policy making, and management of protected areas in developing nations.