Abstract: By PCR amplification and seque ncing and interspecific comparison, we got partial homologous sequences of 18 S rRNA, COI and ITS genes of 6 species of Sargassum. The results showed that:（1） 18 S rRNA homologous sequence length was 1 673 bp, including 1 668 conservative sites, three variable sites, 1 parsimonic information site, and two single mutation polymorphic sites. The average content of T, C, A and G was 26.4%, 21.4%, 24.4%and 27.8%, respectively.（2） COI homologous sequence length was 643 bp, including 567 conserved sites, 76 variable sites, 28 parsimonic information sites, and 47 single mutation polymorphic sites. The average content of T, C,A and G was 40.0%, 17.6%, 19.1% and 23.3%, respectively.（3） ITS homologous sequence length was 1 539 bp, including 1 272 conserved sites, 193 variable sites, 55 parsimonic information sites, and 138 single mutation polymorphic sites. The average content of T, C, A and G was 23.5%, 26.5%, 17.1% and 32.9%, respectively.（4） Genetic distance was calculated based on Kimnra two-parameter model, and phylogenetic trees of 18 S rRNA, COI and ITS gene sequences were constructed by selecting some species of algophyta as exogenous sources. The genetic relationship based on COI and ITS gene was similar with the relationship based on morphology. Sargassum zhangii, Sargassum integerrimum,Sargassum polycystum, Sargassum henslowianum and Sargassum cinereum all belonged to the Subgenus Sargassum.They were close to each other, and first they gathered into one branch, then they gathered into one branch with Sargassum hemiphyllum of the Subgenus Bactrophycus, and gathered into one branch with other subgenera finally. However, the phylogenetic tree constructed with the 18 S rRNA gene was different. In this tree, Sargassum henslowianum and Sargassum hemiphyllum first clustered into one branch, then clustered into one branch with other species of the Subgenus Sargassumm, and finally clustered into one branch with other subgenera. From the conservation degree of sequence, the 18 S rRNA gene was highly conserved and could be used for the identification and classification of the genus above units. COI and ITS were highly polymorphic and could be used for interspecific classification.