Marine animals host diverse microbial communities on their skin that could play a major role for their health. Most inventories of marine animals skin microbiomes have focused on corals and fishes, while the one of cetaceans remains overlooked. A few studies focused on wild or semi-captive cetaceans, making difficult to distinct intrinsic inter- and/or intraspecific variability in skin microbiomes from environmental effects. The analysis of skin microbiome in animals living in environmental controlled conditions is needed to first resolve these variabilities, second to allow faithful comparison with skin microbiome of other marine vertebrates and terrestrial mammals. We used high-throughput sequencing to assess the skin microbiome from 4 body zones of 8 individuals of two emblematic species, the bottlenose dolphin (Tursiops truncatus) and the killer whale (Orcinus orca), housed in captivity in controlled conditions (Marineland park, Antibes, France).