The comparative study of serotypes and virulence genes of Vibrio parahaemolyticus isolated from contaminated aquatic products and infection cases in Beijing not only provided clues for the assessment of food safety risk monitoring, but also offered technical support on the correlation research of aquatic products contaminated by Vibrio parahaemolyticus and clinical infections.Methods Vibrio parahaemolyticus isolates were separated from aquatic product and stool samples of patients with diarrhea. Serotypes were tested by serum agglutination. tlh, tdh and trh gene of the strains were detected by PCR. Results 164 aquatic product samples were collected from July to September. Vibrio parahaemolyticus was isolated from 80 aquatic product samples. Total incidence of Vibrio parahaemolyticus was 48.78%. The incidence of Vibrio parahaemolyticus in sea products was 53.04%, and the incidence of Vibrio parahaemolyticus in freshwater products was 38.78%. The average concentration in sea products was 38.14 MPN/g, and was 66.63 MPN/g in freshwater products. 80 isolates were divided into 9 O serogroups, among which O2 (35.00%), O1 (13.75%) and O5 (12.5%) were the main serotypes. All 80 isolates had tlh gene, only 1 isolate had tdh gene, and no trh gene was detected. From stool samples of sentinel hospital patients with diarrhea, 21 Vibrio parahaemolyticus strains were isolated and identified. Among 21 clinical strains, 13 strains were O3∶K6 serotype, and 6 strains were O4∶K8 serotype, with the ratio of 61.90% and 28.57% respectively. Virulence genotype tdh(+)/trh(-) had 20 strains, tdh(-)/trh(-) had 1 strain, with the ratio of 95.24% and 4.76% respectively.Conclusion China's food safety risk monitoring was mainly to evaluate the occurrence of foodborne illness through monitoring in Vibrio parahaemolyticus in aquatic products. Most of the Vibrio parahaemolyticus strains isolated from aquatic product samples were not pathogenic, but all the Vibrio parahaemolyticus which led consumers to diarrhea carried pathogenic virulence genes, indicating that the current food safety risk monitoring results were not accurate for evaluating foodborne disease outbreaks or sporadic caused by Vibrio parahaemolyticus.