Objective To study the molecular epidemiological characteristics of Vibrio parahaemolyticus isolated from clinical and foodborne isolates collected in Minhang district, and understand the epidemic regularity. Methods 184 Vibrio parahaemolyticus isolates from food-poisoning, sporadic diarrhea patients and food samples from 2007 to 2010 were serotyped. Diplex-PCR was used to detect tdh and trh gene. 102 O3:K6 strains from clinical case and 41 strains from food samples were detected by pulsed field gel electrophoresis (PFGE). Results O3:K6 strains with tdh positive and trh negative were responsible for 88.5% (46/52) of food poisoning cases caused by Vibrio Parahaemolyticus, and O4:K8 strains with tdh positive and trh negative were responsible for the other 5 cases (9.6%). In 63 strains from sporadic diarrhea patients, O3:K6, O4:K8 and O3:KUT with tdh positive and trh negative were responsible for 60.3%(38/63), 19.0%(12/63) and 15.9%(10/63), respectively. 41 strains from food samples belonged to 9 serotypes except O3:K6 and O4:K8, and were both tdh and trh negative. PFGE typing showed that the dominant clone in food poisoning was among O3:K6 strains, and some strains isolated from food poisoning and sporadic diarrhea patients were the same molecular type. All strains isolated from food samples were unrelated with clinical cases. Conclusions There was significant difference between Vibrio Parahaemolyticus isolated from clinical and food samples in the serotype classification , virulence gene and molecular characteristics. A group of close related Vibrio Parahaemolyticus ofO3:K6 strains with tdh positive and trh negative seemed to be prevailing in Minhang.