To investigate the contamination of pathogenic Vibrios in oyster in Beijing markets.Methods Two hundreds of samples were obtained from 80 batches marine products in a wholesale market in Beijing from February to November in 2014. Routine methods were used to detect pathogenic Vibrios in the gills and intestines of oysters. Vibrios parahaemolyticus isolates were serotyped. tdh, trh and tlh genes were detected with real time PCR. Results The isolation rates of pathogenic Vibrios, Vibrio parahaemolytics and Vibrio alginolyticus were 62.50%, 33.75% and 31.25% respectively. The isolation rates of pathogenic Vibrio were 67.50% and 57.50% in gill and intestine samples respectively. Nine serotypes were identified in the isolated Vibrio parahaemolyticus. tdh and trh gene were negative while trh gene was positive in all 27 Vibrio parahaemolyticus. Conclusion A large proportion of oyster sold in market were contaminated by pathogenic Vibrios and Vibrio parahaemlyticus and Vibrio alginolyticus were the predominant species. Oyster without gills and intestine were safer to consume.