Mycobacteria isolated from epizootics of farmed fishes in western Japan were examined for the first time using multigenotypic analysis. By analysis of the sequences of the internal transcribed spacer between the 16S and 23S rRNA genes (ITS) region and the partial 16S rRNA, hsp65 and rpoB genes, M. pseudoshottsii was identified as the causative agent in these infections. Prior to this study, only M. marinum has been known as the causative agent of lethal mycobacterial disease in marine fishes in Japan.