Choke diseases were surveyed in two closely related grass species, Agropyron ciliare var. minus and Agropyron tsukushiense var. transiens, in Shiga Prefecture, Japan. Perithecia and ascospores were not observed in either case. Stromata on A. ciliare var. minus enclosed and sterilized young inflorescences, as in the typical choke symptoms by Epichloë typhina. On the other hand stromata on A. tsukusiense var. transiens thinly covered mature spikes with white epiphyllous hyphae, as in stromata of Ephelis spp. The fungal isolates produced typical Neotyphodium-type conidia. Molecular phylogenetic analyses using the beta-tubulin gene (tubB) indicated that the two Agropyron species are infected with the species grouping into a novel single clade among Epichloë species and they are closely related to a haploid of hybrid Neotyphodium species. The host plant features may be the cause of the differences between stromata of A. ciliare var. minus and A. tsukushiense var.