Vibrio parahaemolyticus is a potentially pathogenic bacterium that occurs naturally in estuarine environments worldwide. This research aimed to investigate the occurrence of V. parahaemolyticus in estuarine environments and determine the virulence profile in an aquaculture environment by molecular techniques and conventional microbiological methods. Sampling was conducted in four estuaries in the State of Ceará (Pacoti, Choró, Pirangi and Jaguaribe), Brazil, between January and April 2009. The analysis included 64 samples of water (n=32) and sediment (n=32) collected from the estuaries. The samples yielded 64 isolates suspected to be V. parahaemolyticus. The isolates were submitted to biochemical identification using a dichotomous key and PCR for the detection of the species-specific tlh gene. Virulence was assessed by testing for urea hydrolysis and β-hemolysis in erythrocytes (Kanagawa phenomenon) and simultaneous detection of the tdh and trh genes. All but one of the isolates (63/64) were confirmed to be V. parahaemolyticus by genotypic detection of tlh gene. The tdhand trh genes were detected in 57 and 19 isolates, respectively. The Kanagawa test was positive for 51 isolates. Only one isolate was positive for urease. The incidence of tdh/trh-positivity was very high in isolates recovered from the environment. The present study demonstrates the need to increase knowledge of the ecology and pathogeny of V. parahaemolyticus