Understanding drivers of trophic partitioning at the community level is an essential prerequisite to the establishment of ecosystem-based management of fisheries. In this study, we identify drivers of trophic partitioning within a community of epipelagic fish and a community of deep-water fishes off Reunion Island. Effects of intrinsic (species identity, etc.) and environmental variables (fishing zone, month) on stomach content composition and stable isotope ratios were tested using regression trees and linear models respectively. Our results demonstrated firstly an independence of both communities, with very few common prey although they occurred in similar localities, and secondly, very different patterns of resources partitioning among each community. The community of epipelagic fish segregated into three trophic guilds composed of species foraging on a limited range of prey. This observation is not consistent with the general view that these high trophic level species are opportunistic and generalist. The habitat seems to be the main driver of deep-water fishes feeding partitioning, which is in accordance with the sound-scattering layer interception hypothesis. Deep-water fishes would distribute in the water column at different depths and all species would feed on the same resources at each depth. The results of this study suggest that fisheries management should be very different for epipelagic (more species-centred) and deep-water fish (more habitat-centred).