The restriction fragment length polymorphism (RFLP) in the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene (rDNA) was analyzed on Fonsecaea pedrosoi isolates kept in the Department of Dermatology, Kanazawa Medical University, Japan. On the bases of the RFLP patterns with Dde I and Msp I, 131 isolates were classified into 5 types (D1-D5) and 4 types (M1-M4), respectively. Combining the RFLP patterns with Dde I and Msp I, the isolates were further classified into 6 rDNA-types which corresponded to the 6 mtDNA-types reported by Kawasaki et al. based on the mtDNA-RFLP patterns, except for a single strain of mtDNA-type 7, which was indistinguishable from mtDNA-type 2. The strains of each rDNA-type formed a clade on the phylogenetic tree constructed from sequences of the ITS regions. ITS-RFLP analysis discriminated F. pedrosoi from 11 other species of pathogenic phaeoid fungi except F. compacta. These results strongly suggest that the typing based on ITS-RFLP is reliable and that F. pedrosoi and F. compacta are conspecific. Compared with mtDNA-RFLP analysis, ITS-RFLP analysis is less tedious, permits simultaneous analysis of many samples and gives equivalent results rapidly. This analysis is therefore useful for typing or epidemiologically investigating F. pedrosoi and for differentiating it from other dematiaceous fungi.