Fishes associated with mesophotic coral ecosystems (MCEs) of the La Parguera shelf-edge were surveyed between 2007 and 2011 using mixed-gas rebreather diving. Fishes were identified and counted within belt transects and roving surveys at 30, 40, 50, 60 and 70 m depth. Vertical transects from 70 to 30 m depth helped determine depth distribution ranges. One hundred and three species were identified at MCEs (40–70 m), with high abundances and species richness, though both varied greatly among transects. Most species at MCEs were common inhabitants of shallow reefs, but some were restricted to mesophotic depths. An additional 15 species were added to those previously classified as indicator species of mesophotic areas in Puerto Rico. The MCE fish assemblage was distinct from shallow areas (30 m), with taxonomic composition, abundance and the proportion of trophic guilds varying with increasing depth. The dominant trophic guild within MCEs was the zooplanktivores, while herbivores dominated shallow reefs. Both herbivores and zooplanktivores responded strongly, and oppositely, to depth. The few herbivores associated with deep MCEs are small-bodied species. The largest changes within the mesophotic fish community along the depth gradient occurred at 60 m, similar to that reported for algae and corals, and seem to represent both a response to reduced light and variations in herbivory. The presence of commercially important fishes at MCEs, many considered to be threatened by fishing pressure in shallow areas, suggests that MCEs are important for the conservation of these species. This study represents the first quantitative in situ observations and descriptions of fishes inhabiting MCEs at depths of 50–70 m in Puerto Rico and highlights the role of MCEs as valuable habitats for reef fishes. The composition and distribution of the MCEs fish community should be incorporated when planning for the spatial management of coral reef resources.