Vibrio parahaemolyticus is one of the most seafood-borne pathogens in China, which may cause acute gastroenteritis. We aimed to investigate the antimicrobial resistance and genotypic relationship of 41 pathogenic V. parahaemolyticus isolates from 342 seafood samples including 248 shrimp, 86 shellfish and 18 fish. These samples were collected from retail markets in Shanghai during March in 2011 to December in 2012. After preliminary screening in Vibrio chromogenic medium, the assumed isolates were confirmed by amplification of tlh, tdh, trh genes through polymerase chain reaction (PCR) and 41 tdh positive V. parahaemolyticus strains were acquired. Besides, pathogenic strains O3:K6 (Vp2) and ATCC33847 (Vp1) were tested in this study as control. By antimicrobial susceptibility testingÿthese pathogenic strains were sensitive to chloramphenicol, 14.63% were resistant to amikacin, and there were varying resistance to amoxicilin-clavulanic, gentamicin, ciprofloxacin, levofloxacin. Analysis by enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) revealed that the isolates could be grouped into six patterns. In conclusion, V. parahaemolyticus was commonly found in retail seafood products from Chinese aquatic market, and a few parts were pathogenic and antibiotic resistant strains which may pose a potential threat to human health.