ABSTRACT.To detect E e St-genome species in Pseudoroegneria and Elytrigia, the primers ES45 (5'-GTAGGCGACGGTTTTCA-3') and ES261 (5'-TCGCTACGTTCTTCATC-3') were designed as sequence characterized amplified region markers based on the 6-base pair indel in internal transcribed spacer 1 (ITS1) regions and conserved sites in the 5.8S regions, respectively. Polymerase chain reaction of ITS fragments in 27 Triticeae accessions was used for amplification with a touchdown thermocycling profile. Two amplicons were purified, sequenced, and aligned. The results indicated that: 1) primers ES45 and ES261 generated the expected products, 2) ITS sequences of E e St-genome species are characterized by a 6-base pair indel, and 3) 13 taxa in Pseudoroegneria and Elytrigia should be included in Trichopyrum. The primers ES45 and ES261 were useful for detecting ITS fragments with 6-bp indel and are helpful for clarifying taxonomic classifications of E e St-genome species in Triticeae.