The occurrence of various Vibrio species in water, sediment and shrimp samples from multiple shrimp farm environments from the east and west coast of India was studied. The relative abundance was higher in west coast farms (ca. 104 cfu/ml water) when compared to the east coast (ca. 102 cfu/ml water). Vibrio alginolyticus (3–19%), V. parahaemolyticus (2–13%), V. harveyi (1–7%) and V. vulnificus (1–4%) were the predominant Vibrio species identified by standard biochemical testing. In some cases, V. cholerae could be found, but all isolates were negative for the cholera toxin (ctx) gene that is associated with choleragenic strains. The biochemical identification of V. parahaemolyticus, the other human pathogen among the species mentioned above, was confirmed by PCR targeting the toxR gene and a 387 bp chromosomal locus specific for this species. Furthermore, the presence of the virulence-associated tdh (thermostable direct haemolysin) and trh (TDH-related haemolysin) genes in the V. parahaemolyticus isolates was also detected by PCR. Only 2 out of 47 isolates were tdh positive and one contained the trh gene. However, since V. cholerae, V. parahaemolyticus and V. vulnificus species are recognized as a major cause of seafood-borne illness, it is important to pay attention to post-harvest handling and adequate cooking.