Abstract: Genetic markers are commonly used to construct systematic trees in studies of phylogenetic relationships among plant taxa. In this study, nine native Elymus species were sampled to analyze their phylogenetic relationships using three genetic markers. Nine Elymus species were separated into two groups: Sect. Turczaninovia(Nevski) Tzvel. and Sect. Elymus. Allozyme markers did not show clear groupings, but Elymus species belonging to the same section or with the same genomic constitution indicated a close relationship. Microsatellite markers did not indicate clear groupings or relationships among the nine Elymus taxa. A significant relationship was found between three genetic markers. A morphological marker was the most significant and gave similar results to the actual relationship of individual species. The second was the allozyme marker and the third a microsatellite marker. Therefore, we suggest that morphological traits are the most direct and efficient genetic markers of Elymus taxa, while allozyme markers are a valuable predictor of the relationship among populations or species, and microsatellites are more suitable for studying inter-population rather than inter-species relationship of Elymus.