The phylogenetic and taxonomic heterogeneity of a rare opportunistic yeast pathogen, Cryptococcus humicolus, was revealed by analysis of the sequence of the internal transcribed spacer (ITS) region. Sixteen strains of C. humicolus showed a wide diversity in their ITS sequences. In addition, their 18S rDNA sequences were determined and used to analyze the phylogenetic relationships among C. humicolus and related yeasts. On trees constructed by the Neighbor-Joining and Maximum Parsimony methods, C. humicolus strains were phylogenetically closely related to each other with the exception of one strain, and they clustered with C. curvatus and Trichosporon species with high bootstrap values. Three C. humicolus strains obtained from humans belonged to the group of Trichosporon serotype I species. The results suggest that C. humicolus is a genetically heterogeneous species which should be reclassified on the basis of DNA sequence data.