We investigated the interspecific relationships and intraspecific variations in the genus Corylopsis using RAPD and single nucleotide polymorphism (SNP) in the internal transcribed spacer1(ITS1), 5.8S ribosomal RNA gene specific in C. glabrescens Franch. & Sav. Differences in species identification between morphological characteristics and RAPD result were noticed in some accessions. All C. glabrescens, C. coreana Uyeki, and C. glabrescens f. gotoana (Makino) T. Yamanaka accessions clustered in one major group. However, they could be divided into five subgroups that are not related to the geographical origins. For example, C. coreana accessions from Korea were clustered with C. glabrescens from Japan. Although grouping based on SNP data does not agree with that by RAPD markers, it revealed the limitation in identification and classification of the genus due to high intraspecific variations in SNP. At SNP positions 464, 465, 466, 467, and 496, most accessions of C. glabrescens and C. coreana have C, G, A, A, and T, respectively. In both analyses, C. glabrescens, C. coreana, and C. glabrescens f. gotoana Japan are closely related and this suggests that nomenclature for these three species should be discussed. Although ITS1 5.8S ribosomal RNA gene can not be used for identification at a subspecies level of C. glabrescens, it proved to be useful to differentiate C. sinensisfrom C. sinensis var. calvescens. It is suggested to use C. glabrescens f. gotoana or C. glabrescens f. coreana rather than using C. coreana.