The genetic variation of Armillaria mellea sensu stricto was studied within and among non-heterothallic populations from Japan and Africa, and heterothallic populations from Europe and North America, using somatic incompatibility tests and RAPD analysis. Non-heterothallic isolates from Japan and Africa were divided into four somatic compatibility (SI) groups (A, B, C and D). SI group A contained half of all Japanese isolates and all African isolates. SI groups B and C each contained four Japanese isolates and D contained one isolate. All European and North American isolates were clearly separated from each other by somatic incompatibility tests. From the RAPD analysis, three distinct groups were separated (non-heterothallic, European and North American groups). The non-heterothallic group was divided into three subgroups (Ia, Ib and Ic). Subgroup Ia and Ib corresponded to SI groups A and B, however, Ic contained SI groups C and D. Subgroup Ia, in which 12 of 14 isolates had the same haplotype, showed a little variation. Non-heterothallic populations were less variable than heterothallic populations. The distribution of the isolates belonging to each SI group overlapped within Japan.