Abstract.. Gene trees based on the DNA sequences of three peroxidase genes of Heterobasidion were compared to previously published trees based on rDNA spacer regions (the two internal transcribed spacer regions and the first intergenic spacer region). This genus of polypored fungi is comprised of three formally recognized species and several intersterility groups within H. annosum, an important root rot pathogen on the Pinaceae. There was congruence among the gene trees in placing H. araucariae and H. insulare basal to the H. annosum complex; and the European pine form, the American pine form, and the fir-spruce form of H. annosum were seen as three separate, strongly-supported lineages in all trees. Within the fir-spruce form, two morphologically and ecologically distinct types are recognized in Europe, the 'S' and 'F' types, which are specialized to spruce and fir, respectively. The 'S' and 'F' types were indistinguishable by their rDNA spacer sequences but were highly divergent in their peroxidase sequences. The 'S' and 'F' types are partially interfertile in laboratory tests, and hybridization events after speciation may explain the similarity of their rDNA spacer regions. The maintenance of divergent extracellular enzymes such as peroxidases, which are critical for wood decay, in the 'S' and 'F' types may be due to selection pressures associated with host specialization.