Perennial Triticeae species of the Thinopyrum genus play a prominent role as a gene pool source for wheat improvement through hybridization. Diploid Th. elongatum with E genome, the basal genome of the genus, received more studies than polyploid Thinopyrum species. Combined the transcriptome analysis of tetraploid and decaploid Thinopyrum with reference genomes of Chinese Spring and Th. Elongatum, we identified 7,397 conserved candidate SNPs between E genome genes and their common wheat orthologs, among which 23 SNP on 1E-7E long and short arms were developed into KASP markers and validated by genotyping and FISH analysis. 52 hybrid lines with different number of E chromosomes or chromosomal arms were detected out from 252 wheat-Thinopyrum elongatum hybrid derivatives. 18 hybrid lines possessed desirable agronomic traits such as salt tolerance and stripe rust resistance. The high-throughput KASP marker system will help to facilitate the introgression of traits from Thinopyrum species into common wheat.