Pulsed-field gel electrophoresis (PFGE) pattern analysis with XbaI restriction enzyme was used to study the genetic heterogeneity of 88 atypical Aeromonas salmonicida strains which were earlier or during this study characterized phenotypically, by ribotyping (ClaI/PstI) and by plasmid profile analysis. The strains of certain ribotypes were also analysed by digestion with SpeI. The strains represented different geographic locations: Finland (72 strains), Iceland (5 strains), Norway (5 strains), Sweden (4 strains) and Denmark (2 strains), and they were from 17 fish species during 1981–97. Thirty-one PFGE genotypes found among these strains correlated well with the ribotypes, and in most cases PFGE pattern analysis subdivided ribotypes into several PFGE genotypes, and further within a PFGE genotype into subtypes. XbaI and SpeI digests produced concordant results. In most cases, PFGE patterns of strains with the same ribotype shared many fragments, suggesting genetic relatedness. PFGE patterns of most Norwegian and Icelandic strains isolated during an approximately 10-year period had the same ribotype and their PFGE patterns shared most fragments, suggesting close genetic relatedness. Moreover, atypical strains of ribotypes B/B and H/H isolated from the same Finnish fish farms had closely related patterns suggesting genetic stability and persistence of these genotypes. Genotype 29 of Achromogenic strains was strongly associated with disease of Finnish arctic char and grayling. PFGE was shown to be a distinguishing method to study the genetic heterogeneity of atypical A. salmonicida. This method is applicable to studies of the epidemiology of these infections.