Abstract. Among the purported relatives of Heterobasidion, the sequences of the internal transcribed spacer region (ITS) of the nuclear ribosomal (rDNA) of H. annosum aligned most closely to Bondarzewia. However, Stereum annosum appeared to be a better outgroup taxon. The intergenic spacer region (IGS) of the rDNA operon was used to find further variation, but numerous insertions and deletions necessitated exclusion of most IGS characters. Heterobasidion araucariae was basal to H. insulare and H. annosum (pine and fir forms) using parsimony analysis. There was strong support for delimitation of the fir form of H. annosum as a distinct species, with isolates from three continents (Japan, Europe and western North America) forming three weakly supported subclades, though the S and F types in Europe could not be separated. The S type appears to be a newly emerging species in Europe especially adapted to Picea abies. The isolates of H. annosum from pine in Europe and H. annosum from pine in America each formed well supported clades, but their relationship to each other and the fir form of H. annosum was not clear. Thus, there are three clades in H. annosum: the fir form, the European pine form, and the American pine form.