To clarify phylogenetic relationships among species of the anamorphic ascomycetous genus Candida with ubiquinone Q-8, we determined complete sequences of 18S ribosomal RNA genes (18S rDNAs) from the type strains of 20 species of the genus Candida and 7 of the teleomorphic ascomycetous genera Pichia and Citeromyces, which have Q-8 as the major ubiquinone. Q-8-forming Candida species were divided into six clusters and were phylogenetically distant from a group of Candida species that included the type species of the genus. One Q-8-forming species from each of the genera Pichia, Citeromyces, or Clavispora was included in five of six clusters. Cluster 1 comprised C. ishiwadae, C. ernobii, C. karawaiewii, C. anatomiae, C. populi, and Pichia holstii. Cluster 2 comprised C. globosa and its teleomorph, Citeromyces matritensis. Cluster 3 comprised C. molischiana and Pichia capsulata. Cluster 4 comprised C. silvanorum, C. sequanensis, C. fennica, C. entomophila, C. homilentoma, C. rhagii, C. gotoi, and Pichia burtonii. Cluster 5 comprised C. fructus, C. musae, and C. lusitaniae (anamorph of Clavispora lusitaniae). Cluster 6 comprised C. stellata, C. lactiscondensi, C. galacta, and C. incommunis and was a heterogeneous group with large interspecific divergence. Pichia pastoris was quite divergent and phylogenetically distant from other Pichia species examined. Pichia methanolica and its synonym, P. cellobiosa, which have both Q-7 and Q-8 as major ubiquinones, were closely associated with Q-7-forming Williopsis salicorniae. Based on this comparative analysis of 18S rDNA sequences, it is evident that Q-8 Candida species and Q-8 Pichia species are polyphyletic.