The prevalence of Salmonella in seafood samples collected from the southwest coast of India was studied by conventional culture and by a DNA based molecular technique, polymerase chain reaction (PCR). While conventional culture techniques detected Salmonella in only 20 out of the 100 samples analyzed, direct enrichment lysate PCR detected 52 as positive for Salmonella. A set of three different PCR primers viz., hns, invA and invE were used. It was observed that hns primer detected Salmonella in a significantly higher number of samples. Fourteen out of nineteen isolates belonged to serovar S. enterica Weltevreden. S. Weltevreden isolates were genotyped yielding 4 different patterns both by RAPD and ERIC-PCR but when combined, the overall results discriminated the isolates of S. Weltevreden into 6 different types. This suggests that genetically diverse Salmonella Weltevreden are prevalent in seafood.