The invention discloses a kind of wheatgrass E. e Genome-specific molecular markers and applications thereof, specifically for diploid R. longa, tetraploid R. longa, durum wheat-tetraploid D. longa diploid 8801, and common wheat-tetraploid Erythorax longus 1E e ‑7E e The chromosomal replacement line was sequenced, and the sequence alignment was performed to obtain a tetraploid Trichoderma 3E e Chromosome-specific sequence, R. longiflorum 3E was developed e Chromosome-specific molecular markers and validated in wheat and its relatives. The specific molecular marker developed in the present invention can not only be used for diploid, tetraploid, and decoploid Trichoderma splendens E e Rapid detection of genomes, also available for all Triticeae containing E e Chromosome or chromosome fragment identification of genomic species, and can accurately identify and distinguish E e and E b Genome, which provides the basis for the phylogeny, germplasm identification, and molecular marker-assisted selection breeding of Triticum species.