Trichaptum fuscoviolaceum is a saprotrophic basidiomycete morphospecies growing on conifers. In the present study, the genetic structure in a circumboreal sample of T. fuscoviolaceum was analyzed using a multilocus sequencing approach. The analyses revealed a complex phylogeographic structure where two main lineages occurred; one European connected to Pinus and another circumboreal group connected to various coniferous hosts. The European group may have resided in South European refugia during the last glaciation followed by a northward range expansion. The circumboreal group probably have migrated into Europe from northeast. In Europe, in areas where the two main lineages occur in sympatry, some specimens possess heterozygous sequences, apparently because allelic versions from both lineages co-exist in the same dikaryons. The presence of alleles from both groups in the same individuals may reflect hybridization as a result of secondary contact between the two main groups. Additional data are needed to conclude whether the two main lineages represent cryptic species. The observed phylogeographic pattern resembles the pattern observed in other wood-inhabiting fungi, which could indicate that general phylogeographic trends exist across species.