Genetic structure of 22 populations of two self-pollinating pasture species, Elymus nutans and E. burchan-buddae collected from various altitudes of the Qinghai-Tibetan Plateau was studied using fluorescence-based amplified fragment length polymorphism technique. Analysis of molecular variance revealed 42.97% and 37.63% among-population variation for the two Elymus species, respectively, indicating that the majority of the total variation presented within populations. This result contradicts the common genetic variation pattern for a selfing plant species: lower generic variation within populations. STRUCTURE analyses of the Elymus populations indicated an evident admixture genetic structure, particularly among neighboring populations from the same region, supporting the hypothesis of considerable seed dispersal among populations. The among-population gene flow promulgated by grazing animals may promote the maintenance of genetic diversity in the pasture species, particularly in small and fragmented populations within a given region. The gene flow promulgated by grazing animals may promote the maintenance of genetic diversity in the pasture species, particularly in small and fragmented populations within a given region.