Phylogenetic relationships of strains belonging to three rare Colletotrichum species in Japan were clarified based on sequences of the rDNA-ITS region and some other genes. Morphological re-examination of the strains was also carried out. Colletotrichum hsienjenchang on a bamboo, Phyllostachys bambusoides, collected in Kanagawa Prefecture, Japan in 2011 was found to produce tufted conidia on the top of polyphialides on PDA medium and large appressoria with a few short projections. Its strain was placed on a branch with C. spaethianum in an rDNA-ITS phylogram, but it was separated on a branch near C. tofieldiae and other closely related species with falcate conidia in phylograms based on actin, chitin synthase 1 or histone 3 partial sequences. Based on the present results, Gnomonia hsienjenchang, a teleomorph of C. hsienjenchang, was transferred to the emended Glomerella. Colletotrichum metake found on another bamboo, Pleioblastus simonii, in Ibaraki Pref., Japan in 2009 was found to form small cylindrical conidia and lemon-shaped appressoria. Although the species has been regarded as a synonym of C. falcatum, the strains were placed on a branch distant from C. falcatum in the rDNA-ITS phylogram. Colletotrichum taiwanense was isolated from a chrysanthemum (Dendranthema grandiflorum) in Okinawa Pref. in 2001, subsequently from the human cornea in Kumamoto, and from a vanilla leaf and a lemon branch in the Bonin Islands, Japan. The species was found to produce arrowhead-shaped appressoria from mycelia, and exceptionally long ascospores with 1-3 septa and large conidia. Strains of the species clustered into a single clade distant from other species of the genus in the phylogram. The three species were demonstrated to be distinct within the genus Colletotrichum by both molecular and morphological evidence in this study.