A new species Elymus margaritae Agafonov, Kobozeva et B. Salomon (Triticeae Dum.) from Altai Mountains (Republic Altai) is described. Data on morphology and some molecular and genetic characteristics of the species are provided. On morphological characters it is most closest to E. komarovii (Nevski) Tzvelev. By results of the ISSR analysis the close relation E. margaritae with StY-genomic species E. fedtschenkoi Tzvelev and E. abolinii (Drob.) Tzvelev was revealed. The new species is distributed on the Krasnaya mountain (Ust-Koksinsky dist.), Katunsky Range and Ukok Plateau. The chromosome number 2n = 4x = 28 was specified.Key words: Triticeae, Elymus, a new species, Republic Altai.