A total of 103 representative colonies from 53 healthy and diseased food fish samples were tested for the incidence of Aeromonas spp. Of which 57% of colonies were positive for Aeromonas spp. by the multiplex PCR (MPCR). On an average, the prevalence was found to be 66% with highest incidence in diseased fishes (76%). About 48% of healthy fish samples were observed to contain Aeromonas. The biomoleculoar identification revealed that the selected virulent hemolytic and enterotoxigenic genes appeared in four different patterns viz. alt; act//hlyA/aer; alt and act//hlyA/aer; ast, alt and act//hlyA/aer, among the MPCR positive isolates of Aeromonas spp. The overall prevalence of the toxin genes alt, act/hlyA/aer and ast among the MPCR positive Aeromonas isolates was found to be 89.8%, 72.9% and 20%, respectively. The biochemical confirmation of the MPCR positive Aeromonas isolates revealed different species in the tested samples belonging to A. hydrophila, A. sobria, A. caviae, A. jandaei, A. veronii, A. schubertii and A. trota and the dominant species was found to be A. hydrophila (48%).