Leymus mollis, a perennial allotetraploid (2n = 4x = 28), known as American dune grass, is a wild relative of wheat that could be useful for cultivar improvement. Shannong0096, developed from interspecific hybridization between common wheat cv. Yannong15 and L. mollis, was analyzed with cytological procedures, genomic in situ hybridization, stripe-rust resistance screening and molecular marker analysis. We found that Shannong0096 has 42 chromosomes in the root-tip cells at mitotic metaphase and 21 bivalents in the pollen mother cells at meiotic metaphase I, demonstrating cytogenetic stability. Genomic in situ hybridization probed with total genomic DNA from L. mollis gave strong hybridization signals in the distal region of two wheat chromosome arms. A single dominant Yr gene, derived from L. mollis and temporarily designated as YrSn0096, was found on the long arm of chromosome 4A of Shannong0096. YrSn0096 should be a novel Yr gene because none of the previously reported Yr genes on chromosome 4A are related to L. mollis. This gene was found to be closely linked to the loci Xbarc236 and Xksum134 with genetic distances of 5.0 and 4.8 cM, respectively. Based on data from 267 F2 plants of Yannong15/Huixianhong, the linkage map of YrSn0096, using the two molecular markers, was established in the order Xbarc236-YrSn0096-Xksum134. Shannong0096 appeared to be a unique wheat-L. mollis translocation with cryptic alien introgression. Cytogenetic stability, a high level of stripe-rust resistance, the common wheat background, and other positive agronomic traits make it a desirable donor for introducing novel alien resistance genes in wheat breeding programs, with the advantage of molecular markers that can be used to confirm introgression.