Technical Abstract: Elymus L. is the largest and most complex genus in the Triticeae with approximately 150 polyploid perennial grass species occurring worldwide. We report here the first genetic linkage map for Elymus. Backcross mapping populations were created by crossing caespitose Elymus wawawaiensis (EW) (Snake River wheatgrass) and rhizomatous Elymus lanceolatus (EL) (Thickspike wheatgrass) to produce F1 inter-specific hybrids that were then backcrossed to the same EL male to generate progeny with segregating phenotypes. EW and EL are both allotetraploid species (n=14) containing the St and H genomes. A total of 387 backcross progeny from four populations were genotyped using 399 AFLP and 116 EST-based SSR/STS markers. The resulting consensus map contained the expected number of 14 linkage groups. EST-based SSR/STS markers with homology to rice genome sequences were used to identify Elymus linkage groups homoeologous to chromosomes one through seven of wheat. The frequency of St-derived genome markers on each linkage group was used to assign genome designation to all linkage groups, resulting in the identification of the seven St and seven H linkage groups of Elymus. This map also confirms the alloploidy and disomic chromosome pairing and segregation of Elymus and will be useful in identifying QTLs controlling perennial grass traits in this genus.