The paper examines the Protected Area Management Systems (PAMS) on Biodiversity Conservation and Sustainable Development (BCSD) of 28 protected areas (PAs) in Mindanao, Philippines, focusing on the contexts, inputs, processes and outcomes. Of the nineteen variables, eight were found to be significantly correlated to BCSD of the PAs. Path analysis was used to determine direct, indirect and net effects of the variables to BCSD. The study concluded that placement of optimal PA staffing and resource management implementation are both crucial in achieving BCSD. It necessitates critical and positive collaboration with Protected Area Management Board (PAMB), resource generation contributing to the operation of the PA and community participation in management. The longer the PA under protection, the better is its contribution to BCSD. Policy recommendations were formulated in the areas of institutional, economic, technical, community participation and PAMB operations.