Data were collected from the Caribbean and the Great Barrier Reef to quantify the taxonomic and functional composition of fish assemblages that characterise coral reef, seagrass and mangrove habitats, in order to explore the potential effects of biogeographic history and environment on assemblage composition. In each habitat, the area with the highest fish species diversity was sampled, i.e. the reef crest, the seagrass edge, and the mangrove edge (in this study mangroves were represented by clear-water mangroves). Four timed swim transects were conducted at each sampling location. Each transect consisted of a 20 minute timed swim recording any fishes > 10 cm in total length on a 5 m wide belt transect. This was followed by a 10 minute timed swim as the diver swam back towards the starting point surveying fishes < 10 cm within a 1 m wide transect. In all cases surveys were swum at a constant pace and averaged approximately 235 m in length for the 20 minute swim and 117 m for the 10 minute swim. In total, 108 surveys were conducted (46 reef, 36 seagrass, 26 mangrove). All abundance data were standardised to the number of individuals in each family per 100 m2. The functional data was based on allocating fishes into one of 14 broad functional entities based on body size (above or below 10 cm) and feeding guild (herbivorous/detritivorous, herbivorous-macroalgae, invertivorous-sessile, invertivorous-mobile, planktivorous, macroinvertebrates and fish, and omnivorous).