Objective To investigate the contamination of Vibrio alginolyticus in seafood sold in Beijing and compare the different identification method. Methods After enrichment with alkaline peptone water(APW), a loopful from APW culture was streaked on thiosulfate citrate bile salts sucrose agar(TCBS)and CHROMagar Vibrio simultaneously. Typical colonies of Vibrio alginolyticus were identified with reverse transcription polymerase chain reaction(RT-PCR).The isolated 95 Vibrio alginolyticus strains were also identified with VITEK 2 COMPACT GN card and rpoB gene sequencing. Results Vibrio alginolyticus strains were isolated from 116 seafood which were collected randomly from markets in Beijing. The result indicated that the detection of Vibrio alginolyticus in seafood was high in Beijing, about 82%(95/116). CHROMagar Vibrio media got higher detection rate than TCBS media, which were 82%(95/116) and 72%(83/116) respectively. RT-PCR result were in good accordance with that of rpoB gene sequencing, while VITEK 2 COMPACT GN card could only identify 32.6%(31/95) of the isolated strains as Vibrio alginolyticus. Conclusion The contamination of Vibrio alginolyticus in seafood was serious in Beijing. CHROMagar Vibrio media was better than TCBS media for isolation. RT-PCR could give a more precise result than VITEK.