Marine sanctuaries are increasingly being promoted as tools for conservation and fisheries management. This study investigates the effects of protection over 19 years on substrate composition and fish communities in four marine sanctuaries and corresponding non-sanctuary areas in the Philippines and examines the importance of community support, management measures and enforcement of regulations on these ecological effects. Between 1981 and 2000, substrate cover variables were measured using line transects with scuba and snorkel surveys, and fish censuses (identification to family level) were conducted using scuba within a 500 m2 area. Semi-structured interviews collected data on community support for the sanctuaries, and observations and interviews established management and enforcement aspects of the sanctuaries. Over time, all sanctuaries showed improvements, or maintenance of, ecological variables compared with pre-enforcement times, with maintenance of hard coral cover and average increases of 8.3% in fish species richness and 54.9% in fish abundance. In comparison, non-sanctuary areas showed maintenance of the status quo or declines in ecological variables. However hard coral cover, fish abundances and fish species richness showed significant declines as well as increases in sanctuary areas. Community, management and enforcement factors were significantly related to positive ecological trends in sanctuary areas; management and enforcement were related to a wider variety of ecological factors than community score. Community support was significantly related to an increase in hard coral cover in deep areas. Enforcement of regulations was significantly related to an increase in abundance of fishery target fish species in sanctuary areas, and simple management measures were significantly related to an increase in abundance of large predators. Supportive communities that voluntarily implemented sanctuary regulations, improved enforcement, and small discrete cohesive communities may have facilitated the process of building this community support. Well-enforced sanctuaries that showed an increase in abundance of target species may have contributed to the maintenance of fish yields in adjacent non-sanctuary areas. The effects of sanctuary implementation varied on a case-by-case basis, influenced by environmental, biological, physical and human factors. However, a combination of community support, management measures and enforcement of regulations contributed towards positive ecological trends in sanctuary areas.