Edwardsiella tarda is one of the most significant bacterial pathogens to fish aquaculture worldwide. Here, we evaluated antibiotic resistance profiles, virulence genotypes and phylogenetic relationship of 30 Edwardsiella tarda isolates derived from cultured fish in Japan. The E. tarda isolates were phylogenetically (16S rRNA) clustered into two clads. The isolates of clad 1, which were mainly originated from olive flounder Paralichthys olivaceus and Japanese eel Anguilla japonica, had all of the known 11 virulence genes (ank, katB, LuxS, citC, astA, evpP, mukF, gadB, fimA, hlyA, esa) for E. tarda and mostly one or two of three aminoglycoside resistance genes, i.e. aac(6')-Ib, armA and strA-strB, if exists. In contrast, the isolates of clad 2, which were mainly originated from red seabream Pagrus major and black seabream Acanthopagrus schlegelii, lacked four (ank, katB, LuxS, citC) of the 11 virulence genes and, eight of them harbored mainly a β-lactam resistance gene (bla CTX-M). In infection experiments with zebrafish, representative isolates of the clad 1 showed higher virulence than those of the clad 2. These results reveal that the virulence profiles may be applicable for prediction of pathogenicity in fish. Phylogenetic analysis revealed that E. tarda isolates derived from olive flounder and red seabream are ancestor differentiated.