The genus Elymus L. sensu lato includes Roegneria, Elymus, Hystrix, Sitanion and Kengyilia, and they are very important group in the tribe Triticeae. However, the phylogenetic relationships and taxonomic status of them are still in dispute. The ITS sequences were obtained and analyzed for their phylogenetic relationships by using Maximum Parsimony (MP) and Bayesian Inference (BI) methods. The main results were as follows: (1) Most species in Roegneria, Elymus and Sitanion were clustered in the St clade with diploid St genome species, and it was difficult to distinguish the species in Roegneria and Elymus; (2) The polyploid species with St genomes in the St clade were divided into three groups, which suggests that there exists differentiation of St genome in polyploids; (3) Most species of Kengyilia have only P-type of clone and clustered with diploid Agropyron species, which may suggest that Kengyilia is a valid genus; (4) Hy. patula, the type species of Hystrix was clustered with species of Elymus, while Hy. duthiei ssp. duthiei, Hy. duthiei ssp. longearistata, Hy. coreana and Hy. komarovii were grouped with diploid Psathyrostachys species. It indicated that Hy. patula is distinct related to other Hystrix species, and it is reasonable to treat Hystrix patula as Elymus hystrix and other species in Hystrix should be transferred to Leymus; (5) The “clones bias” in ITS sequences are widespread in the allopolyploid species.