Although mesophotic coral reef ecosystems (MCEs) are widespread and diverse, they remain largely unexplored. The Caribbean MCEs are among the most studied in the world, but detailed information regarding Cuban MCEs is limited. In this study we present the first analyses of the ichthyofauna of the Cuban MCEs based on data from a research cruise in June 2017. Forty-two sites were sampled around the Archipelago of Cuba using a Remotely Operated Vehicle at depths between 30 and 180 m. Overall, 151 species were observed, including 13 threatened species. Differences in ichthyofauna were observed between marine protected areas (MPAs) and unprotected areas, with greater abundances and species richness inside national parks. Invasive lionfish had greater abundances on the north coast, while the south coast had greater abundances and richness of threatened and commercially valuable species. A detailed analysis (Generalized Lineal Model) showed effects of depth, protection level, reef type (seamount or fringing reef), and region on abundance (as fish observed per minute), but no interaction between them. A transition was observed in the fish assemblages between the 30–60 m and 60–100 m depth ranges. Species abundance and richness decreased with increasing depth. The most represented families of commercial importance (Serranidae, Lutjanidae, and Carangidae) were well represented in the upper, middle, and lower areas of the MCEs, but dominated in deeper areas. The percentage of herbivores in the fish assemblage decreased with increasing depth, contrary to what was observed with piscivores and invertebrate feeders/piscivores. Twenty-seven functional groups were identified, with cryptic micro-invertivores and cryptic planktivores being the most abundant, while roving macro-invertivores and roving piscivores were the most functionally redundant. This research constitutes a valuable contribution to the study and management of ichthyofauna in Cuba and highlights the effectiveness of MPAs in the conservation of fish biodiversity.
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