Root-associated microbial consortia in alpine tundra ecosystems are unknown for the majority of plant species. Nitrogen (N) enrichment can facilitate plant productivity and fungal growth, but in certain conditions can negatively affect diversity and survival. The main goal of this study was to describe fungal symbionts associated with two dominant plants (Geum rossii and Deschampsia cespitosa) and to evaluate the effect of N fertilization on root- associated fungal communities. Forty-two plants were collected from four different treatments: control with no N added, N fertilized, N fertilized/D. cespitosa removal, and D. cespitosa removal/no N added in the years 2008 and 2010. The study site was located at the Niwot Ridge Long Term Ecological Research (LTER) site in Colorado. Roots were harvested from each treatment and stained to quantify fungal colonization. One hundred and ninety pure cultures of endophytic fungi were isolated on potato dextrose agar and fungal isolates were identified by sequencing the Internal Transcribed Spacer rDNA. Plant roots were highly colonized by arbuscular mycorrhizal fungi and dark septate endophytes. Microscopy data from 2008 and 2010 showed an increase in percentage of fungal colonization (primarily in vesicle and spore colonization) in N fertilized plots when compared to control plots. Identification of fungal isolates showed that G. rossii is mainly colonized by fungi in the phylum Ascomycota including ericoid mycorrhizae in the order Helotiales such as Cryptosporiopsis ericae, the dark septate fungus Phialocephala fortinii and other unidentified species. Potential effects of these fungal symbionts on various seeds and young plants were examined. Most isolates did not show any effect or germination or plant growth but two isolates Thielavia sp. and Leohumicola sp. showed pathogenic activity. The study showed that fungal communities are highly variable and their effects depend on a complex combination of biotic and abiotic factors.