Objective To survey the contamination of Vibrio parahaemolyticus in shellfish in 2009, and to study the type of virulent genes in isolates from shellfish and clinical samples, in order to find out the epidemic rules of Vibrio parahaemolyticus in Zhoushan. Methods Eighty shellfish samples were collected from Zhoushan markets in four seasons. Fifty isolates from shellfish and 18 isolates from parts of sporadic diarrhea cases and food poisoning patients were serotyped, and the virulent genes, including tdh、trh、orf8 and toxRS/new genes, were detected by PCR. Results The positive rate of Vibrio parahaemolyticus was not significantly different among samples collected in spring (85%), summer (80%) and autumn (75%), while the positive rate in winter (10%) was significantly lower than other seasons. The virulent tdh, toxRS/new and orf8 genes were all negative in shellfish isolates, and only virulent trh gene was detected in two isolates collected in winter. The virulent tdh, toxRS/new and orf8 genes were positive in 14 clinical isolates and trh gene was positive in another one clinical isolate. The 4 virulent genes were all negative in the remaining 3 isolates. The results showed that Vibrio parahaemolyticus strains in 14 of 18 clinical isolates (77.78%) were pandemic strains, of which 13 strains (92.86%) were categorized as type O3:K6, and one was categorized as type O1:KUT. Conclusion The contamination of Vibrio parahaemolyticus was serious in shellfish in spring, summer and autumn; the shellfish contaminated by Vibrio parahaemolyticus maybe the main source for human diarrhea; A group of Vibrio parahaemolyticus strains with positive O3:K6 type tdh、orf8 and toxRS/new genes was endemic in Zhoushan.