A total of 100 samples (50 fish samples each from freshwater and marine source) were collected and analyzed through cultural and PCR methods. In cultural method positive result for V. parahaemolyticus was 36% in case of freshwater fish and 48% in case of marine fish where as in PCR it was 40% and 52% respectively. Out of 50 samples of freshwater fish 4 samples were having tdh and 3 samples were having trh gene where as in marine fish samples the result was 8 samples (tdh) and 5 samples (trh) respectively. The efficiency of PCR was high compared to traditional cultural methods. Hygienic practice and surveillance with molecular study may reduce the risk of food borne infection in near future.