This study primarily aimed to measure the level of effectiveness on the management of locally declared marine protected areas in Bohol, Philippines as perceived by the local government officials and leaders of fishermen association. Method applied in this study was descriptive with the use of adopted and enhanced survey questionnaire. Four hundred three (403) respondents from local government officials and leaders from fishermen association in 27 communities in 12 coastal municipalities. Findings showed that the over-all level of perceived level of effectiveness on the management of marine protected areas was effective if based on the four parameters, vis-à-vis, (a) establishment, (b) strengthening, (c) sustainability, and (d) institutionalization. Intruders from neighboring communities was the top most problem, followed by insufficient budget allocation of the local government units, weak enforcement of fishery laws, and poor participation of local fishermen of the management of marine protected areas. The over-all results were effective. The study concluded that some improvements are needed to effectively manage the marine protected areas in Bohol, Philippines.