Fishers across the Indo-Pacific target deep-reef species, but there is insufficient information for fisheries management in marine environments deeper than 50 m. We hypothesized that population structure and community assemblage of fishes would vary with depth and habitat type over a depth range of 50-260 m on the Great Barrier Reef. Further, we used fish otoliths (ear-bones) to identify regional stock structure at spatial scales of 10s-1000s of kilometres from Indonesia to Tonga. We found that depth, topography and hardness of substrate were good predictors of species distribution. Mesophotic fishes had varying degrees of habitat specialization. Closely-related species (of the same genus) had different habitat preferences and specialization, likely due to niche differences (i.e. diet, depth range). Otolith chemistry for three commercially-valuable eteline snappers showed regional spatial patterns. There were strong inter-species differences in otolith composition, indicating potential variation in growth, diet and habitat use. Some locations showed elemental signature differences between neighbouring Pacific island nations, suggesting separate stocks, but these varied among species. Spatial delineations among stocks can be enhanced with otolith elemental chemistry. This study demonstrated deep-reef fish communities vary by habitat type, but exhibit inherent vulnerability in the narrow depth ranges over which many species are found.