We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.Vibrios are gram-negative, usually motile rods, are mesophilic and chemoorganotrophic, and have a facultatively fermentative metabolism (5). They are generally able to grow on marine agar and on the selective medium thiosulfate-citratebile salt-sucrose agar and are mostly oxidase positive. Vibrios belong to the Gammaproteobacteria according to 16S rRNA gene sequence analysis. These bacteria are found abundantly in aquatic habitats and in association with eukaryotes. Associations established by vibrios range from mutualistic, e.g., Vibrio fischeri-bobtail squid (26), to pathogenic, e.g., V. cholerae-humans (45). Probiotic Vibrio strains for fish and shellfish have also been documented (44).The current family Vibrionaceae comprises the genera Enterovibrio (2 species), Grimontia (1 species), Photobacterium (7 species), Salinivibrio (1 species), and Vibrio (64 species). The novel species Photobacterium rosenbergii and Enterovibrio coralii have recently been proposed to encompass isolates associated with coral bleaching (41). Several new Vibrio species, mainly in the phylogenetic neighborhood of V. harveyi, V. halioticoli, V. splendidus, V. tubiashii, and V. fluvialis, have been described in the last few years, with V. neonatus, V. ezurae (28), and V. ponticus (22) being the most recent ones. V. harveyi, V. splendidus, and V. tubiashii are frequently associated with disease in different spe...