Utilizing allozyme markers, genetic relationships were investigated for 40 populations representing 10 Elymus species indigenous to the Tibetan and Inner Mongolian Plateau regions. From the allozyme analysis, the genetic diversity within populations (He) was very low, ranging 0.0160–0.1680. At the species level, Nei's gene diversity and Shannon's information index ranged 0.0800–0.2528 and 0.1173–0.3769, respectively. Allzoyme locus diversity across the 40 populations suggested that polymorphic loci contributed to 72.1% of the total allozyme diversity (HT = 0.2979) while only 27.9% was indicated within populations. A low occurrence of gene flow among populations (Nm), based on Gst calculations, was calculated to be 0. 1932. With respect to potential gene flow (Nm) at the species and population level, a lower frequency of gene flow occurred between populations within species than between species. In general, species of E. geminatus and E. glaucus, and the nationally protected plant E. breviaristatus, indicated the lowest level of genetic variability. From a geographic standpoint, accessions obtained from different regions indicated a wide range of genetic diversity values. Populations indigenous to the Tibetan Plateau suggested a higher level of genetic diversity than those sampled from the Inner Mongolian Plateau.