Coral colony size-frequency distributions (SFDs) can elucidate demographic differences among coral species and their responses to environmental drivers. However, studies on species-specific demography of coral colonies in the Coral Triangle are rare despite the knowledge about the regional variability of reef conditions. Coral reefs in the Southern Philippine Sea biogeographic zone (SPS) frequently experience natural (e.g. typhoons) and anthropogenic disturbances. Coral colony sizes in the SPS may vary with depth within a small-distance (< 1 km) scale and with the presence of marine protected areas (MPA) but studies rarely demonstrate this variability in Indo-Pacific coral reefs. Here, we examined the colony density, SFDs and the extent of partial mortality of scleractinian coral species Porites cylindrica and P. rus in Leyte Gulf, SPS. Field surveys were conducted within and outside (locations) the Bagonbanua Marine Reserve and Fish Sanctuary, SPS and between depths (3 m and 8 m) of each location. High densities of colonies of both species occur at shallow depths. We found that SFDs and colony sizes were similar between depths and between locations (inside and outside of the MPA). The percent partial mortality of only P. cylindrica colonies was significantly different between depths and between locations with low mortality at 3 m inside the MPA. Our study showed small-sized colonies that could be linked to high colony recruitment, fragmentation and potential recovery from disturbances.