Coral reefs are in dire need of effective governance, yet the science and planning of coral reef protected areas largely stem from wealthy, developed nations, with very different social, economic, and cultural characteristics than the nations in which most coral reefs occur. Much has been written about coral reefs and the use of marine protected areas (MPAs) as a management tool, but emerging trends and recommendations have not been adequately synthesized for the context of developing nations. We found that 60% of studies on MPA design and planning are from North America, Australia, Europe and the Mediterranean. As a result, many recommendations about how best to design, implement and manage coral reef protected areas may need to be adapted to address the needs of other nations. Based on the literature and our experiences, we review three emerging trends in MPA design and management, and relate these to the context of coral reef developing nations. First, MPA design is evolving to merge community (usually bottom-up) and regional (usually top-down) planning approaches. Second, the increasing recognition that social and ecological systems are tightly coupled is leading to planning and management of MPAs that better incorporate the human dimensions of reef systems and their linkages with reef ecology. Finally, there has been a trend toward adaptive management of MPAs and the emergence of related ideas about adaptive planning. These three trends provide crucial and much needed opportunities for improving MPAs and their effectiveness in coral reef nations.