Primary tropical montane forests along the eastern Andes contribute significantly to the storage of carbon and to the designation of the tropical Andes as a biodiversity hotspot. Despite their remoteness, these unique ecosystems are increasingly experiencing the effects of different global change factors. Of particular concern, given the adaptation of eastern Andean forests to infertile soils, is the increased deposition rate of nitrogen and phosphorus resulting from the intensification of human activities in neighboring regions. Tropical montane forest trees rely on arbuscular mycorrhizal fungi (AMF) to obtain nutrients from the scarcely available pool found in eastern Andean soils. In addition to AMF, it is believed that tropical trees interact with a broad range of fungal taxa that range from facultative saprobes to specialized plant pathogens. Given root associated fungi stand at the interphase of soil and plants and are directly involved in the flow of nutrients, studying their response to an increased availability of N and P can give insight into the response of the ecosystem to this disturbance. The work presented in this dissertation is a compendium of three scientific contributions. Two of them document the response of root associated fungal communities to increased availability of nitrogen and phosphorus and one is a methodological viewpoint that critically assesses the suitability of current sampling strategies to study soil microbial communities. The empirical studies collected mixed root samples from a fertilization experiment seven years after the manipulation started. This experiment simulated the atmospheric deposition rates expected for the eastern Andes, by fertilizing the forest floor at a rate of 50 kg N ha-1 yr-1 and 10 kg P ha-1 yr-1. To increase the external validity of the manipulation, the experiment was deployed in forests occurring along an elevation gradient (1000–3000 m above sea level) that represents the typical transition from pre-montane to upper montane forests observed in the eastern Andes. High-throughput sequencing was employed to characterize AM and non-AM fungal communities recovered from DNA extracted from mixed root samples. Based on previous studies, it was hypothesized that chronic fertilization will decrease AMF diversity and community composition given plants will invest less C in the symbiosis. As the ambient N and P availabilities shift with elevation and it is likely that AMF clades have distinct nutritional niches, it was further hypothesized that site and clade specific responses will be observed. Regarding additional clades of root associated fungi, it was expected that fertilization will reduce diversity and alter community composition. It was assumed that the pool of soil fungi available to interact with roots decreases, since it is unlikely all fungal taxa are able to regulate their elemental stoichiometry to maintain homeostasis with the altered soil stoichiometry elicited by fertilization. AMF alpha diversity decreased with elevation and there was a strong turnover of operational taxonomic units (OTUs) across sites, which indicates AMF taxa have narrow environmental niches. Non-AM fungal communities were taxonomically rich, mostly including phylotypes within Ascomycota, Basidiomycota and Mortierellomycota. Guild structure was also diverse, and mostly included fungal saprobes and plant pathogens. Fertilization consistently altered AMF community composition along the elevation gradient, but only reduced Glomeraceae richness. Compositional changes were mainly driven by increases in P supply while richness reductions were observed only after combined N and P additions. Taxonomic richness of non-AM fungal communities was not affected by fertilization, neither at the kingdom nor at the phylum level. In contrast, community composition shifted, particularly among Ascomycota and after the addition of P. These findings suggest that, unlike AMF, non-AM fungal communities are less sensitive to shifts in soil nutrient availability. Overall the findings reported in this dissertation expand our understanding about the response of root associated fungi to increased nutrient availability in tropical systems. Sensitivity of AMF communities to P fertilization is in line with previous literature and causes concern in light of the current trends of atmospheric deposition. We confirmed that tropical montane trees interact with diverse fungal communities, and these appear to be robust to the addition of nutrients. Despite the fact that we characterized root associated fungal communities at a resolution that has never been achieved before in this region, we are still lacking the most basic understanding of the functional roles and trophic modes of most members of these communities. Hence, we hope the patterns revealed in these studies inspire further exploration of tropical montane fungi.