Evaluating the management effectiveness of marine protected areas (MPAs) has been a continuing challenge in marine conservation in the tropics. This paper describes the process involved, the chosen indicators and the selected results of the evaluation of management effectiveness of three MPAs in the Calamianes Islands, Palawan Province, Philippines. The evaluation was a participatory process that involved several institutions: academe, an externally-funded project, local governments, national government agencies and research organizations. Twenty-three indicators were used for evaluation: six biophysical indicators that largely measured the status of capture fisheries and coastal habitats; eight socioeconomic indicators that largely assessed the economic status and the perceptions of coastal communities; and nine governance indicators that measured the various facets of MPA management. Key lessons learned indicate the need to correlate the perceptions of coastal stakeholders with scientific findings as some perceptions did not reflect the results of biophysical surveys. We illustrate that a multidisciplinary approach and engagement of key stakeholders provides a comprehensive assessment and consensus for measuring the success of MPAs.