The PCR technique based upon randomly amplified polymorphic DNA (RAPD) markers using 10-mer oligonucleotide primers was used to investigate the phylogenetic relationships among 33 isolates of Heterobasidion annosum belonging to the intersterility groups F and S. The F isolates originated from Italy, the S isolates from the Italian Alps, northern Europe and North America. The presence or absence of some bands was shown to be population-specific. The North American S group and the European S group differed significantly from each other, but within the latter group there were no significant differences between the Italian S and the northern European S populations, with as much similarity within these populations as between them. More DNA polymorphisms appeared within European F and S groups than in the North American S group. The North American S group appeared to be more closely related to the European S group than to the F group. The isolates of the Italian F population seemed to be most closely related to the Italian S isolates and then, in decreasing order, to the northern European S and North American S isolates. The order of genetic similarity was inversely correlated with the mating frequency in vitro obtained in an earlier study.