Geum and Deschampsia were both highly colonized by arbuscular and ericoid mycorrhizal fungi. Dark septate fungi were also observed. Culturable endophytes of Geum were dominated by fungi in the order Helotiales that included several hyaline ericoid and pseudomycorrhizal fungi such as Phialocephala fortinii. Root-associated fungi were closely related to fungi found in roots of alpine ericaceae plants, Antarctic plants such as Colobanthus quitensis and Deschampsia antartica and other plants in alpine tundra. Deschampsia isolates were less abundant and roots were mainly colonized by bacteria. N fertilization increased AMF and ericoid colonization of Geum roots, but did not alter the colonization of Deschampsia roots. N fertilization also decreased dark septate fungi for both plant species. Our findings partially support our hypothesis: fungal communities associated with Geum increased and potentially shifted towards more parasitic fungi. However, Deschampsia colonization did not change due to N fertilization. Although further quantification of the benefits and costs of particular fungal groups is needed, our results suggest that shifts in fungal associations may contribute to the declines in plant species abundance due to N enrichment.