Objective To study the serotype distribution of Vibrio parahaemolyticus clinical isolates and aquatic products isolates during 2009-2012 in Shanghai. Methods Using slide serum agglutination test to detect the serotypes of Vibrio parahaemolyticus from 622 clinical and 176 aquatic samples. Results Among 622 clinical isolates, 27 serotypes were identified. The predominant serotype was O3∶K6 (61.7%). It was shown that 176 aquatic strains could divide into 9 serum groups. The predominant serotype O3∶K6 among clinical isolates was detected in two aquatic products. Conclusion The serotypes among clinical isolates and aquatic products showed high diversity. The predominant serotype O3∶K6 among clinical isolates appeared in aquatic product representing a public health risk and requiring epidemiological and ecological monitoring to ensure safety.