The invention belongs to the field of crop genetic improvement, comprising the following steps of: sequencing the specific segments of common wheat and a common wheat-elytrigia elongata addition line to obtain a mass of common wheat and elytrigia elongata sequences, carrying out comparative analysis on the sequence data by computer software to obtain a mass of elytrigia elongata 1E chromosome specific segmental sequences, randomly selecting 8 sequences, and successfully developing 5 elytrigia elongata 1E chromosome specific molecular markers such as one of SED ID NOs.1, 4, 7, 10 and 13. The markers not only can be used for detecting the elytrigia elongata 1E chromosome, but also can be used for the assistant selection of the molecular markers in the wheat resistance breeding. Furthermore, the SLAF-seq technology-based successfully developed elytrigia elongata chromosome specific molecular markers can provide an important reference for the molecular marker development technologies of the other species, and provide an important application basis for the molecular breeding, the system evolution and the germplasm resource identification.