The South China Sea (SCS) is a biodiversity hotspot, however, most biodiversity surveys inthe region are confined to shallow water reefs. Here, we studied the benthic habitat andfish 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 ofIslands) in the eastern SCS (also called the West Philippine Sea) using diver-based surveymethods. Mean coral genera and fish species richness ranged from 17–25 (per 25 m2) and11–17 (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. Locationdifferences were associated with the variability in benthic composition, wherein locations withhigher hard coral cover had higher coral genera richness and abundance. Locations withhigher algae and sand cover had higher diversity and density of fish herbivores and benthicinvertivores. Fishing efforts may also have contributed to among-location differences as thehighly exploited location had the lowest fish biomass. The low variation between depthsmay be attributed to the similar benthic composition at each location, the interconnectivitybetween depths due to hydrological conditions, fish motility, and the common fishinggears used in the Philippines that can likely extend beyond SWRs. Results imply that local-scale factors and anthropogenic disturbances probably dampen across-depth structuring incoral genera and fish species assemblages.