Coral reef fishes are fishes that are found inhabiting coral reefs and its proximities. Fishes that have evolved to live here are extremely dependent on the healthy ecosystem for their survival. As such reef fishes are a good indicator of the reefs’ health. Marine protected areas are globally recognised as a powerful tool to manage living marine resources from the ever increasing exploitation threats, and to control the degradation of their ocean habitat. Two hypotheses of this project are: 1) The commercially exploited reef fishes of Sabah exhibit a low level of intraspecific genetic diversity in areas where commercial fishing is permitted; 2) Coral reef fish populations in Sabah exhibit high genetic diversity in established marine reserves. Two MPAs are surveyed in this study; these are Tunku Abdul Rahman Park, and the proposed Tun Mustapha Park. The latter is not yet a fully protected marine area; nevertheless, the local youths are already providing voluntary ad-hoc protection in several areas near their coastal village.