Abstract: We used phylogenetic analysis to compare the ITS2 and psb A-trnH sequences of the plant of the genus Salix samples,so as to explore the genetic diversity and genetic relationship of these resources. Extract genomic DNA of the genus Salix and Tamarix chinensis samples. The ITS2 and psbA-trnH gene sequences of each samples were amplified and sequenced by PCR. The intraspecific and interspecific genetic distances and the neighbor joining（NJ）methods were used to construct phylogenetic trees. According to the phylogenetic tree of ITS2. S. pentandra,S. rorida,S. linearistipularis and S. schwerinii formed a monophyletic clade,distinguished from the same genus. Phylogenetic tree constructed by psbA-trnH sequences were unable to distinguish the genus Salix samples from different geographical sources. Therefore,ITS2 sequence was suitable for the authentication,and would provide a certain reference for the subsequent development and research of the plant of genus Salix.