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. Moh´eli Marine Park was designed to address threats to the marine environment and is a model for co-management practices. The Moh´eli Marine Park illustrates use of area-based management tools, namely marine reserves nested within a marine park, for biodiversity conservation and local fisheries management. The authors conducted a year-long evaluation of the park implementation process, including community and fisher participation. After 3 years of operation with 80% local community control, the park maintains a small staff to monitor sea turtle nesting beaches, reef health, fisheries, and uninhabited islets and to guide ecotourists and educate visitors. Analysis revealed successes and shortcomings of the co-management approach. Successes included local communities empowered to participate in natural resource management, increased local involvement in conservation initiatives, and use of traditional knowledge when scientific information was unavailable. A flexible project that incorporates local knowledge and participation as well as education and capacity building of all stakeholders is a viable approach. 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.