Many grass species in Triticeae serve as important gene pools for forage and cereal crops breeding. Extensive natural and artificial interspecific hybridization have given rise to different ploidy of Triticeae species (Wang et al. 1994). The St genome was defined in diploid Pseudoroegneria species, and is a donor genome of at least seven genera including Douglasdeweya, Roegneria, Elytrigia, Thinopyrum, Elymus, Kengyilia and Pascopyrum according to different taxonomic systems (Wang et al. 1994; Yen et al. 2005). In the past decades, numerous studies on species containing St-chromosome were focussed on genomic relationship and molecular phylogeny based on molecular markers including chloroplast DNA, high-copy nuclear genes, singlecopy nuclear genes, as well as genomic in situ hybridization (GISH) (Kellogg and Appels 1995; Mason-Gamer et al. 2002; Mason-Gamer 2005). Among these species, Thinopyrum intermedium with genome constitution of E1E2St (Wang et al. 1994) or JJsSt (Chen et al. 1998) was widely used in wheat breeding programme (Chen 2005; Li and Wang 2009). Molecular markers, particularly genome-specific markers, are useful in identifying the genome constitution of the unknown species, and also provide efficient tools to check the target alien genes transferred to wheat (Schwarzacher et al. 1992; Wang et al. 2010). Only a few St-chromosomespecific RFLP (Zhang et al. 2001), SCAR (Liu et al. 2007) and ISSR (Zeng et al. 2008) markers were developed to identify genome composition and the individual St-chromosomes. However, the most available markers are lacking in information on the corresponding homologous linkage group relative to wheat. Based on the orthologous gene conservation between rice and wheat, Ishikawa et al. (2007) reported an array of PCR-