We investigated the influence of microsite and establishment factors on the distribution of Botrychium pumicola Coville ex Underw. (Ophioglossaceae), an obligate mycorrhizal fern restricted to specialized volcanic habitats, predominately pumice, in the Cascade Range of central and southern Oregon and northern California. The fragmented distribution of this threatened species and its absence from suitable habitat is of conservation concern. At eight subalpine and one alpine site, plots with and without B. pumicola were compared for biotic and abiotic variables. Botrychium pumicola populations occurred with diverse perennial plants. Nearest neighbor analysis showed a clumped dispersion of B. pumicola with associated plants. Botrychium pumicola spores were found in soils of seven plots with and two without B. pumicola. In plots with B. pumicola, soil potassium was higher while soil density and soil temperatures were lower than in plots without B. pumicola. Airborne spores, collected in spore traps, were dispersed up to 10 m from source plants. Microsite factors (soil nutrients, soil density, nearest neighbor dispersion) and dispersal limitations are likely key factors influencing the distribution of Botrychium pumicola. Narrow spore germination requirements combined with dispersal limitations may influence population expansion of obligate mycorrhizal ferns such as B. pumicola.