The pathogenicity of aeromonads produces due to exotoxins such as cytolytic enterotoxin, hemolysin or aerolysin, lipases and proteases. Rapid detection of A. hydrophila cytolytic enterotoxin (AHCYTONE) gene and their characterization has proven importance so that proper and rapid preventive and control measures could be taken up to reduce mortality and loss in fish culture. The main objective of the present study is to genetic identification of AHCYTONE positive Aeromonas hydrophila. Strains were isolated from fishes from different fish market in West Bengal and water samples from different river and ponds. Initially strains were identified by their phenotypic and biochemical characterization. Due to contradiction of those results, molecular characterization was done by polymerase chain reaction, which is proved a suitable and rapid diagnostic tool for identification and characterization of A. hydrophila. We have also evaluated the potential risk to human health that this finding can represent by determining the presence of the cytolytic enterotoxin gene in such isolates.