Diversity is among the various aspects of reef fish assemblages that are expected to change with protective management. Reef fish diversity in terms of richness (number of species per 500m²), abundance (ind/500m²) and biomass (g/m²) were determined for six (6) reef sites in Tawi-Tawi, at the southwestern tip of the Sulu Archipelago, and in Danajon Bank, Bohol, in central Philippines in 2006 and 2008. At each reef site, reef fish within a 500m² area were censused (identified, counted and their sizes estimated) in 6-12 stations following standard methods. Changes in reef fish assemblages in the two areas were examined and observed patterns were compared. The results are related to patterns in reef habitat structure and to local fisheries and are discussed in the context of recovery potential of reef fish assemblages in protected areas.