The southeastern coast of Florida, USA supports a substantial recreational fishery, yet little is known of the coral reef ecosystem or fisheries resources past 50 m depth. Fish assemblages associated with low-relief substrate and three vessel reefs between 50 and 120 m depth off southeast Florida were surveyed by remotely operated vehicles providing the first characterization of the mesophotic fish assemblages in the region. Two distinct assemblages were observed on low-relief substrate and high-relief vessel reefs. A total of 560 fishes of 42 species was recorded on 27 dives on low-relief substrate, and 50 152 fishes of 65 species were recorded on 24 dives on three vessel reefs. Small planktivorous Anthiinae fishes and several economically valuable species were common on vessel reefs but rare on low-relief substrate. Fish assemblages on vessel reefs more closely resembled those found at similar depths in high-relief natural areas off east-central Florida and the Gulf of Mexico than those associated with adjacent low-relief habitat or nearby coral reef tracts. From a fisheries perspective, these results provide limited support to the hypothesis that in deep-water regions with limited relief, vessel reefs may provide an opportunity to increase fish diversity and abundance by creating high-relief habitat without compromising adjacent fish assemblages.