By reducing soil organic matter and litter input, land-use changes are predicted to decrease total soil fungal diversity, but at functional levels this have been poorly studied. It is expected, though, that increasing disturbance decreases saprotrophic and mycorrhizal fungi biodiversity. This study aimed to determine the effects of land-use changes on the phylogenetic and functional diversity of soil fungi in the Southern Andes. We assessed the fungal communities of Andosol topsoil at 1 cm and 10 cm soil depth. The soil samples were obtained from a gradient of anthropogenic disturbance; specifically, plots were located within pristine forest, overstory-managed, and clearcut conditions. We used a cultivation-independent molecular barcoding approach to assess fungal diversity and identify 1,173 OTUs from which 401 were assigned to a functional guild. While we found higher phylogenetic richness in clear-cut conditions, these soils had higher relative abundances of plant pathogen fungi and lower relative abundances of saprotrophic and ectomycorrhizal fungi compared to the other treatments. The opposite pattern was found in pristine forest. Thus, fungal species richness itself does not seem to reflect ecosystem health. Interestingly though, the lower phylogenetic diversity found in pristine forest was compensated by a higher diversity of fungi involved in nutrient cycling. © 2017, Sociedad Chilena de la Ciencia del Suelo. All rights reserved.