Abstract: Forage grasses (Poaceae) often harbour endophytes belonging to the Neotyphodium and Epichloë (Clavicipitaceae, Ascomycota) genera. Neotyphodium endophytes, the asexual state of Epichloë species, helps to protect cool-season grasses against biotic and abiotic stresses including drought, disease, herbivory and parasitism and enhance aboveground and belowground vegetative and reproductive growth. There is little information on colonial diversity of asexual endophytes isolated from Elymus species in northwest Chinese. In the present study, different geographic populations of Elymus species were tested using the aniline blue screening method; 15 endophyte strains were isolated from endophyte positive plants. The average growth rate (on potato dextrose agar) of the isolated strains was 0.41-0.85 mm/day and was correlated with altitude. Endophyte strains isolated from regions below an altitude of 3000 m grew faster than strains isolated from regions above 3000 m. The colonial morphology of endophyte strains isolated from regions above 3000 m was similar whereas the colonial morphology of endophyte strains isolated from lower altitudes differed. In addition, the phylogenetic trees showed that endophytes collected above 3000 m were clustered whereas endophyte strains from lower altitudes demonstrated a star-like topology. The results will provide a theoretical basis for the identification of endophyte from northwest Chinese Elymus species.