Whitebark pine ( Pinus albicaulis Engelm.) is unique as the only stone pine in North America. This species has declined 40%–90% throughout its range owing to blister rust infection, mountain pine beetle, fire suppression, and global climate change. However, intact mature and old growth forests still exist in the Greater Yellowstone Ecosystem (GYE) at high timberline elevations. This study addresses the urgent need to discover the ectomycorrhizal (ECM) fungi critical to this tree species before forests are further reduced. A study of mature whitebark pine forests across five mountain ranges in the Northern GYE confirmed 32 ECM species of fungi with the pine by sporocarp occurrence in pure stands or by identification of mycorrhizae with ITS-matching. Boletales and Cortinariales ( Cortinarius ) comprise 50% of the species diversity discovered. In Boletales, Suillus subalpinus M.M. Moser (with stone pines), Suillus sibericus Singer (stone pines), Rhizopogon evadens A.H. Sm. (five-needle pines), Rhizopogon spp. (pines) and a semi-secotioid Chroogomphus sp. (pines) are restricted to the hosts listed and are not likely to occur with other high elevation conifers in the GYE. The ascomycete generalist, Cenococcum geophilum Fr., was the most frequent (64%) and abundant (51%) ECM fungus on seedling roots, as previously reported for high elevation spruce-fir and lower elevation lodgepole pine forests in the GYE. The relative importance of the basidiomycete specialists and the ascomycete generalist to whitebark pine (and for seedling establishment) is not known, however this study is the first step in delineating the ECM fungi associated with this pine in peril.