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The variability in reef‐fish species assemblages was examined at three geographic locations in the Philippines (Apo, Abra and Patn), each showing varying levels of disturbances (low to high) at two depths, shallow‐water reef (SWR; 8–20 m) and the upper mesophotic coral ecosystem (MCE; 30–35 m). Fish species assemblages varied among locations and between depths. Differences in fish assemblages among locations corresponded to the variability in benthic assemblages and levels of disturbances, wherein locations with higher coral cover and less disturbances had the highest fish species richness, abundance and biomass. Variation in fish assemblages between depths was also associated with changes in benthic assemblages and possibly inaccessibility to local fishing techniques. Fish species richness decreased with depth in all locations, but biomass increased only in the MCEs of Apo and Abra, which is a similar pattern exhibited in many MCEs. Our results suggest that despite location differences, depth had a relatively consistent influence on fish species assemblages, particularly in locations exposed to low and intermediate disturbance. Under high disturbance, MCEs exhibit similar vulnerability to SWRs. [ABSTRACT FROM AUTHOR]

The Philippines is located within an area of high reef biodiversity. However, it is vulnerable to the overexploitation of marine resources, which has reduced the abundance of many species, particularly large reef fish and marine turtles in the shallow reef areas (< 30 m). There is a need to assess the populations of these marine animals in the mesophotic coral ecosystems (> 30 m). The objectives of the study were (1) to determine the macrobenthic invertebrates and megafauna communities across the different reef type and depth; (2) compare species composition of macrobenthic invertebrates and megafauna communities across reef type and depth; and (3) to determine the benthic cover across reef type and depth. Macrobenthic invertebrates and megafauna communities in the upper mesophotic zone (30-40 m) in Apo Reef Natural Park, Philippines were sampled using 15 min Underwater Visual Census (UVC). We observed 'regionally' rare macroinvertebrates and megafauna such as Holothuria fuscogilva, Thelenota ananas, Bolbometopon muricatum, Cheilinus undulatus, Alopias pelagicus, Triaenodon obesus, and Eretmochelys imbricata, which may be attributed to the long term (21 years) protection provided by Apo Reef. Interestingly, there were no significant differences in species richness, abundance and species composition across reef types and depths, probably because of horizontal and vertical movement of megafauna and the relatively similar benthic composition. This study provides one of first quantification of macrobenthic invertebrate and megafauna communities in mesophotic reefs, which is data deficient in the coral triangle; thus, contributing to the budding mesophotic research program in the region. [ABSTRACT FROM AUTHOR]