Technical Abstract: Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Knowledge of their genome compositions is pivotal for efficient utilization of this vast gene pool in germplasm enhancement programs. Several cleaved amplified polymorphic sequence (CAPS) markers were developed to distinguish the Eb, Ee and R genomes. With the aid of disomic addition lines of wheat, all seven chromosomes of Eb-, Ee- and R-genome were confirmed to carry these genome-specific CAPS markers. Thus, the identified CAPS markers are useful to detect and monitor the chromosomes of these 3 genomes. This study also provides evidence suggesting that some Purdue and Chinese germplasm lines developed for barley yellow dwarf virus (BYDV) resistance are different from those developed in Australia. Furthermore, Thinopyrum intermedium and Th. ponticum were shown to have different genome constitutions. Sequence analyses of the ca. 1272bp sequences, containing Ty3/gypsy retrotransposons, from the Eb, Ee and R genomes also shed light on the genome evolution of these 3 genomes.