We performed the first taxonomic characterization of vibrios and other culturable microbiota from apparently healthy and diseased Brazilian-endemic corals at the Abrolhos reef bank. The diseases affecting corals were tissue necrosis in Phyllogorgia dillatata, white plague and bleaching in Mussismilia braziliensis and bleaching in Mussismilia hispida. Bacterial isolates were obtained from mucus of 22 coral specimens originated from the Abrolhos Bank (i.e. Itacolomis reef, Recife de Fora reef and Santa Barbara Island) in 2007. Vibrios counts in the water and coral mucus were approximately 104 cfu ml−1 and 106 cfu ml−1 respectively. One hundred and thirty-one representative vibrio isolates were identified. Most vibrio isolates (n = 79) fell into the core group using the pyrH identification marker. According to our analysis, diseased corals did not possess a unique vibrio microbiota. Vibrio species encompassed strains originated from both apparently healthy and diseased corals. The pathogenic potential of representative vibrio isolates (V. alginolyticus 40B, V. harveyi-like 1DA3 and V. coralliilyticus 2DA3) were evaluated in a standardized bioassay using the animal model Drosophila melanogaster and caused 25–88% mortality. This is the first taxonomic characterization of the culturable microbiota from the Brazilian-endemic corals. Endemic Brazilian corals are a reservoir of the vibrio core group. Vibrio alginolyticus, V. harveyi and V. coralliilyticus are dominant in the mucus of these corals and may be a normal component of the holobiont.