India with its rich diversity in fisheries resources, contributes greatly in the production and export of the same. Farm raised shrimps particularly Penaeus vannamei continues to be an major export item in the international market. India has a wide variety of market including USA, Japan, South East Asia, China, etc. It has been reported that there has been rejection of the consignment of the farmed shrimp exported from India mainly due to the presence of Salmonella. Hence, an attempt was made to examine the incidence of Salmonella in the water and sediment samples of creeks of shrimp farms in Nagapattinam District, Tamil Nadu. The water and sediment samples were collected from 10 creeks of shrimp farm region namely Vettar (Nagore), Karuvelankadai, Chinnathumbar, Periyathumbar, Velankanni, Vettaikaraniruppu, Vellapallam, Kallimedu, Sembodai and Thoppudhurai in the Nagapattinam District to detect the presence of Salmonella. The Isolation of Salmonella was done by using conventional USFDA method and biochemical confirmation tests. The molecular identification of biochemically positive isolates of Salmonella was done by targeting invA gene, amplified at 284bp. Of the 40 samples collected from creeks, 25% of samples were biochemically positive for Salmonella and only one sample was PCR positive for Salmonella. Among the ten biochemically positive samples, five each were from water and sediment samples respectively. The biochemically positive water samples were collected from Karuvelankadai, Vettaikaraniruppu, Chinnathumbar, Velankanni and Thoppudhurai creeks. On the other hand the biochemically positive sediment samples were collected from Chinnathumbar, Vellapallam, Karuvelankadai, Periyathumbar and Vellapallam creeks. The PCR positive water sample collected from Thoppudhurai creek of Nagapattinam District.