Coenogonium isidiatum (G.Thor & Vězda) Lücking was confirmed to occur in central Honshu, Japan based on the taxonomic examination of herbarium specimens. Although it was reported from Shikotan Island which is under the Northern Territories Issue, there are no other records from Japan. This species was collected from Shizuoka and Nagano Prefectures at elevations between 1220 and 1700 m where it grew on the bark of Fagus crenata or on mosses scattered on the bark, and also on rock with mosses scattered on the surface. The ITS rDNA sequences of Japanese materials show high identity with those of C. isidiatum registered in GenBank.