Coral reef marine protected areas (MPA) are widely distributed around the globe for social and ecological reasons. Relatively few of these MPAs are well managed. This review examines the governance of coral reef MPAs and the means to improve coral reef MPA management. It highlights common governance challenges, such as confused goals, conflict, and unrealistic attempts to scale up beyond institutional capacity. Recommendations, based on field experience and empirical evidence from around the world, are made for best practices at various stages of MPA implementation.