Abstract: Forty-seven strains of Vibrio were isolated from sea area of 7 islands of Xisha Yongle Islands.The 16 S rDNA,HSP60 and gyrB genes of the 47 strains were amplified, and their sequences were compared in GeneBank and then phylogenetic trees were constructed.The results showed that neither 16 S rDNA nor HSP60 could be used to identify the species of Vibrio.Both gyrB1 and gyrB2 primers could only amplify the target sequence of 6 strains.gyrB3 primers could amplify the target sequence of all the 47 strains, and the phylogenetic trees were successfully constructed.Species could be identified using gyrB3 primers.The 47 strains of Vibrio were divided into 7 species.Five strains of Vibrio was isolated in Yagong Island which had the highest diversity.Two species were isolated in both Shiyu and Antelope reef which had the lowest diversity.In this study, a reliable molecular identification method for marine Vibrio was established.The obtained strains enriched the microbial library of the South China Sea and provided materials for future research and teaching.