A survey of mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) in 51 wild strains from different geographical populations of the basidiomycete Lentinula edodes was carried out to examine genetic relatedness. Thirty-eight of the 51 strains were from Japan, seven from Papua New Guinea, four from New Zealand, one from Borneo, and one from Thailand. EcoR I or BamH I digests of mtDNAs from these strains produced 24 and 12 distinct RFLP patterns, respectively. By combining the RFLP patterns obtained with the two endonucleases, mtDNAs from the 51 wild strains of L. edodes could be assigned to 28 different mtDNA phenotypes. A similarity matrix calculated between all pairs of mtDNA phenotypes based on the presence or absence of comigrating restriction fragments was analysed with UPGMA and Fitch-Margoliash analyses. Results of both analyses were highly consistent and showed that the mtDNA phenotypes of L. edodes could be divided into five major clusters, each of which accommodates a geographically distinct population. The phylogenetic relationships among the natural populations of L. edodes deduced from the present study were consistent with previous isozyme analyses. This suggests that L. edodes includes some distinct groups with genetic divergence in both mitochondrial and nuclear genomes.