Technical Abstract: Basin wildrye (Leymus cineneus) and creeping wildrye (L. triticoides) are out-crossing perennial grasses native to western North America. These divergent species are generally adapted to different habitats, but are often found together and have potential to form fertile hybrids. Cultivars of both species are used in agriculture and conservation. However, patterns of genetic structure and gene flow have not been tested. Thus, multi-locus AFLP genotypes and chloroplast DNA sequences were evaluated from 536 L. cinereus and 43 L. triticoides plants from 224 locations of western United States and Canada. Bayesian-cluster analysis detected possible admixture between species, but only 2.2% of the plants showed more than 10% introgression. However, three L. cinereus races corresponding to the Columbia, Rocky Mountain, and Great Basin regions were distinguishable. Approximately 91% and 732% of the Columbia and Great Basin accessions were octoploid, respectively, whereas 82% of the Rocky Mountain accessions were tetraploid. Approximately, 35.9% and 7.1% of the AFLP variation was apportioned among species and races, respectively. Conversely 8.0% and 11.0% of the chloroplast DNA sequence variation was apportioned among species and races. Linkage disequilibrium between AFLP markers and correlation between genetic and geographic distances were detectable within L. cinereus, but diminished within races.