Escherichia coli is an indicator species of bacteria to determine faecal/sewage contamination in food and water. Some strains of E. coli have the potential to be pathogenic to humans. The food and its environment should regularly be monitored for the prevalence of pathogenic E. coli. A study was conducted to determine the prevalence of pathogenic E. coli from different fish markets and landing centres in three districts of Kerala, India. Isolated E. coli were pathotyped as enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC) and Shiga toxin producing E. coli (STEC) by PCR, targeting the genes viz., bfpA, eaeA, stx1 stx2, Lt1, Lt2, ST, phoA and rfbeO157. Pathogenic E. coli was found in 23.4% of the 123 seafood samples screened and ETEC, EPEC, and STEC were prevalent in 18.6, 4.0 and 0.8% of the samples respectively.