ABSTRACTThe genetic heterogeneity of the close relativesVibrio anguillarumandVibrio ordalii, both serious pathogens of fish causing extensive losses in aquaculture, was studied. Eight housekeeping genes, i.e.,atpA,ftsZ,gapA,gyrB,mreB,rpoA,topA, andpyrH, were partially sequenced in 116 isolates from diverse fish species and geographical areas. The eight genes appear to be under purifying selection, and the genetic diversity in the total data set was estimated to be 0.767 ± 0.026. Our multilocus sequence analysis (MLSA) scheme identified several widespread clonal complexes and resolved the isolates, for the most part, according to serotype. Serotype O2b isolates from diseased cod in Norway, Ireland, and Scotland were found to be extremely homogeneous. Horizontal gene transfer appears to be fairly common within and between clonal complexes. Taken together, MLSA andin silicoDNA-DNA hybridization (DDH) calculations suggest that some isolates previously characterized asV.ordalii, i.e., 12B09, FF93, FS144, and FS238, are in factV. anguillarumisolates. The precise taxonomic situation for two isolates from Atlantic cod that display several traits consistent withV. ordalii, i.e., NVI 5286 and NVI 5918, and a single environmental strain that was previously considered to representV. ordalii, i.e., FF167, is less clear.IMPORTANCEIt is still being debated whetherV. anguillarumandV.ordaliirepresent separate bacterial species. Our study addresses this issue and elucidates the degree of genetic variability within this group of closely related bacteria, based on a substantial number of isolates. Our results clearly illustrate the existence of different populations among putativeV.ordaliiisolates. On the basis of additional full-length genomic analysis, we conclude that most environmental isolates previously identified asV.ordaliilie firmly within the speciesV. anguillarum. Whilebona fidefish-pathogenicV.ordaliiisolates display a very close genetic relationship withV. anguillarum, they combine a clearly divergent evolutionary pattern with clear phenotypic differences. The study also highlights the need for further characterization of fish-pathogenic isolates from the northern Atlantic region that share phenotypic characteristics withV. ordaliibut are genetically closer toV. anguillarum. The retention of taxonomic distinctions between the phenotypically different groups of bacteria is of practical advantage to microbial ecologists and veterinarians.