Coral reefs across the world face significant threats from fishing and climate change, which tends to be most acute in shallower waters. This is the case off Pemba Island, Tanzania, yet the effects of these anthropogenic stressors on the distribution and abundance of economically and ecologically important predatory reef fish, including how they vary with depth and habitat type, is poorly understood. Thus, we deployed 79 baited remote underwater videos (BRUVs) in variable water depths and habitats off Pemba Island, and modeled the effects of depth and habitat on abundance of predatory reef fish. Predatory reef fish types/taxa were significantly predicted by depth and habitat types. Habitats in relatively deeper waters and dominated by hard and soft corals hosted high species richness and abundance of predatory reef fish types/taxa compared to mixed sandy and rubble habitats. The findings add to the growing evidence that deep waters around coral reefs are important habitats for predatory reef fish. Thus, careful management, through effective area and species protection measures, is needed to prevent further depletion of predatory reef-associated fish populations and to conserve this biologically important area.