Mycoheterotrophic plants are nonphotosynthetic and must form a relationship with a mutualistic fungus and an autotrophic host to acquire carbon. In this study, identity of fungal associates of Pterospora andromedea in the south-central Rocky Mountains was determined. Although P. andromedea has been found to associate with at least three Rhizopogon species groups throughout its range in North America, it was found to exclusively associate with the Rhizopogon salebrosus species group in the Rocky Mountains. In addition, the genetic structure of R. salebrosus was examined. The data support the presence of two genetic lineages within the R. salebrosus species group that exhibit strong biogeographic distribution linked to historic conifer association with Pinus contorta and Pinus ponderosa . A zone of secondary contact between the two lineages was also identified along with a number of putative hybrids. ► In this study, all mycobionts of Pterospora andromedea were Rhizopogon salebrosus . ► Two separate lineages were identified by network analyses in ITS and RPB2 . ► The separate lineages associated with either Pinus ponderosa or P. contorta . ► A third group comprised of the putative hybrids was also identified.