Aims: The study was undertaken with the objective of understanding the virulence-associated genes of the CTX and TCP gene clusters in environmental isolates of Vibrio cholerae , an important human pathogen, isolated from the aquaculture environment. The involvement of the omp U gene in conferring bile resistance in these isolates was also evaluated. Methods and Results: The V. cholerae isolates were tested by PCR and fluorescent antibody test for O1 (Ogawa and Inaba) and O139 serotypes. All isolates were found to be non-toxigenic V. cholerae confirmed by their positive PCR reaction for tox R but negative for ctx , zot and tcp gene. The hly A gene was detected in 85% of the strains and omp U in 77%. The results on the bactericidal effect of bile salts suggest that omp U may play a role in conferring bile resistance in non-O1/non-O139 strains. Conclusion: The results of the study indicate that most environmental strains lacked the CTX and TCP gene clusters. However, most isolates had the hly A gene indicating the potential of these environmental strains to cause mild gastroenteritis. It was also observed that strains lacking omp U showed less tolerance to bile salts. Significance and Impact of the Study: Information on virulence factors of V. cholerae associated with aquaculture environment and products would be of value in risk assessment for human health.