To estimate the phylogenetic relationships between Hystrix and its related genera (Poaceae: Triticeae), the sequences of the single-copy nuclear gene Pgk1 were analyzed for five Hystrix taxa, together with three Pseudoroegneria (St) species, two Hordeum (H) species, two Psathyrostachys (Ns) species, four Elymus (StH) species, five Leymus (NsXm) species, Thinopyrum bessarabicum (Eb), and Lophopyrum elongatum (Ee). Sequence analysis indicated that an 81bp Stowaway insertion occurred in the Pgk1 sequences of L. arenarius and Psa. juncea, and a 29 bp Copia insertion occurred in the Pgk1 sequences of Hy. duthiei, Hy. duthiei ssp. longearistata and L. akmolinensis. Phylogenetic analysis indicated that: (1) Hy. patula was closely related to Pseudoroegneria, Hordeum, and Elymus; (2) Hy. duthiei, Hy. duthiei ssp. longearistata, Hy. coreana, and Hy. komarovii were closely related to Psathyrostachys and Leymus. Based on these results, it is reasonable to transfer Hy. patula from Hystrix to Elymus, and to combine Hy. duthiei, Hy. duthiei ssp. longearistata, Hy. coreana, and Hy. komarovii into Leymus.