Background : The surface of marine animals is covered by abundant and diversified microbial communities,whichhave major roles for the health of their host.While such microbiomes have been deeply examined in marineinvertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received lessattention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers arestill mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystemservices while they are increasingly affected by human activities. Here, we investigated these knowledge gapsanalyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in thesame area.Results : Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on averagemore than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fishindividual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of thehost and its ecological traits.Conclusions : These results highlight that coral reef biodiversity is greater than previously appreciated, sincethe high diversity of macro-organisms supports a highly diversified microbial community. This suggest thatbeyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could alsolead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.