Marine protected areas (MPAs) have been a popular strategy for protecting and managing coral reefs in the Philippines for the last two decades. However, a great majority of these protected areas are reported to be ineffective and are failing to achieve the goals and objectives for which they were established. As the numbers of MPAs increase, the need for systematic, long-term monitoring of these areas becomes apparent. The purpose of this paper is to make recommendations for monitoring MPA effectiveness of two community-based MPAs in Verde Island, Philippines. Based on findings, it is evident that management lacks the staff, funding, and enforcement capabilities to effectively manage established MPAs at Verde Island. Clearly, there is a need for better and more effective management of these MPAs, and a program to monitor and evaluate management effectiveness can help achieve this goal. Given the stated implicit objectives of the MPAs at Verde Island, a number of recommendations are provided for monitoring MPA effectiveness. These recommendations include: 1) Define and prioritize an explicit set of goals and measureable objectives; 2) Measure the impact of protection on fishery yields; 3) Monitor biological indicators of the coral reef ecosystem; 4) Ensure a sufficient replication of permanent transects with and outside MPAs; 5) Monitor the effectiveness of surveillance and compliance with MPA regulations; 6) Measure local awareness and understanding of MPA regulations; 7) Measure benefits from tourism; 8) Monitor level of stakeholder participation and satisfaction in management activities; 9) Measure effectives of education, information, and awareness programs.