In this study, sixteen Aeromonas (A.) hydrophila and A. caviae isolates obtained from fish in Ankara, Turkey were described and compared with two American type strains (A. hydrophila ATCC 7966 and A. caviae ATCC 15468) and characterised by various methods including biochemical, physiological tests and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Whole cell protein (WCP) profiles of these isolates were analyzed using SDS-PAGE. We concluded that the study showed that there was a similar clonal group origin of the A. hydrophila isolates and the reference strain (ATCC 7966). Likewise, there was also a similarity between the A. caviae isolates and the reference strain (ATCC 15468). The results show that SDS-PAGE may be an efficient method to differentiate Aeromonas isolates.