It will provide useful information for germplasm DNA fingerprint identification, phylogeny by using ITS sequences analysis of Elymus sibiricus and E.nutans. The results show length of ITS, ITS1, 5.8S and ITS2 are identity, and they are 604bp, 222bp, 164bp and 218bp in order, and G C content are 62.25-63.08%, 62.16-63.06%, 59.76%, 64.22-65.60% in order. Except for 5.8S, base sites have some vary, some variable sites are species-specific and can be used as DNA molecular markers of Elymus sibiricus and E.nutans. Percent identity of the seven ITS squences is 98.7%-99.8%, divergence is 0.2-1.3, they have conservation, and not recent differentiated groups. Phylogenetic analysis indicates that different sources of the same species, speed of DNA changes and the number of base subsititue are different, but the same species belongs to group together, and reflects the intraspecific genetic stability in further.