The diversity of Tricholoma matsutake basidiomata and their distribution across Japan was investigated, for the first time, by using PCR-RFLP and sequencing. Eight distinct IGS1 rDNA types were identified by using the restriction endonuclease Cfr13I. Four (A, B, G, H) were characterized by one IGS1 dominant sequence, which could then be recorded by direct sequencing of the PCR products. In contrast, the four other types (C, D, E, F) were characterized by up to more than four codominant IGS1 copies that needed to be cloned before sequencing. Among the copies, one was always exhibiting the RFLP pattern of type A basidiomata. Pairwise nucleotide variation among IGS1 spacer copies, recorded in RFLP types A, B, C, D, F, and H, was very low and never exceeded 1·9%. In contrast, type G emerged and its IGS1 spacer sequence exhibited at least 10·6% nucleotide variation compared with all other types. While the data recorded suggests a higher genetic diversity in the southern than in the northern part of Japan, no host/matsutake ribotype specificity could be evidenced. In Japan, the T. matsutake basidiomata belonging to RFLP type A were by far the most frequent. They were found at most sites and were usually the most abundant at each site. Furthermore, this predominance persisted over time during ca 50 years. The dominant RFLP type A may represent the original Japanese population while the other genotypes may have been more recently introduced.