Coniophora arida and C. olivacea (Coniophoraceae, Boletales) are widespread wood-decay fungi in temperate and boreal regions, occurring both in buildings and natural environments. Genetic variation and geographic structure among isolates of C. arida and C. olivaceae were investigated in this study, with an emphasis on North America. Multilocus sequencing of three DNA regions revealed three main lineages in C. arida and six in C. olivacea, some of which might represent cryptic species. Most of the lineages are present in North America, mainly in allopatry, suggesting recent or ongoing geographic speciation. One of the C. arida isolates included a high number of heterozygous sites and might represent a hybrid between two cryptic C. arida lineages. The data indicate out-crossing reproductive modes in both C. arida and C. olivacea. Together with other recent investigations of Coniophora species our data suggest that the genus comprises a significant number of cryptic species and is much more diverse than previously deduced from morphological characteristics.