The South China Sea (SCS) is a biodiversity hotspot, however, most biodiversity surveys in the region are confined to shallow water reefs. Here, we studied the benthic habitat and fish assemblages in the upper mesophotic coral ecosystems (MCEs; 30–40 m) and SWRs (8–22 m) at three geographic locations (Luzon Strait; Palawan; and the Kalayaan Group of Islands) in the eastern SCS (also called the West Philippine Sea) using diver-based survey methods. Mean coral genera and fish species richness ranged from 17–25 (per 25 m2) and 11–17 (per 250 m2) in MCEs, respectively; although none of these were novel genera/species. Coral and fish assemblages were structured more strongly by location than by depth. Location differences were associated with the variability in benthic composition, wherein locations with higher hard coral cover had higher coral genera richness and abundance. Locations with higher algae and sand cover had higher diversity and density of fish herbivores and benthic invertivores. Fishing efforts may also have contributed to among-location differences as the highly exploited location had the lowest fish biomass. The low variation between depths may be attributed to the similar benthic composition at each location, the interconnectivity between depths due to hydrological conditions, fish motility, and the common fishing gears used in the Philippines that can likely extend beyond SWRs. Results imply that local-scale factors and anthropogenic disturbances probably dampen across-depth structuring in coral genera and fish species assemblages.