The taxonomic relationship of 32 species in the genus Candida Berkhout was examined by characterizing the restriction patterns of nuclear internal transcribed spacers and coenzyme Q types. A matrix of 116 characters was generated from 32 species and seven restriction endonucleases, and phenetically analyzed. Unweighted pair-group arithmetic average (UPGMA) analysis was used to construct the phenograms. The 32 species fell into five major groups corresponding with their genetic relationships. The medically important Candida species clustered together, except C. glabrata. Almost identical restriction patterns were observed between C. hydrocarbofumarica and C. blankii, C. stellatoidea, and C. albicans, and C. steatolytica, and C. inositophila due to synonymous or opposite mating type relationships. The members in each group did not show the same coenzyme Q types, whereas the closely clustered members in each group exhibited the same coenzyme Q types. The results of this study, analyzing ITS-RFLPs and the coenzyme Q type, provided an insight into the various genetic origins of Candida species as well as their genetic relationships.