Here, we examined the colonization by fungal root symbionts in the cultivated Andean grain Chenopodium quinoa and in 12 species that dominate plant communities in the Bolivian Altiplano above 3,700 m elevation and explore for the possible relationships between fungal colonization and fine root proportion. The 12 most abundant species in the study area were consistently colonized by AMF and DSE. In contrast, the annual Andean grain C. quinoa showed negligible or absence of mycorrhizal fungi colonizing roots. On the other hand, C. quinoa, Junelia seriphioides and Chersodoma jodopappa were infected to a varying degree by the root pathogen Olpidium sp. We observed no relationship between AMF and DSE colonization and proportion of fine roots in the root system, but instead, the ratio between DSE and AMF colonization (ratio DSE/AMF) negatively related with proportion of fine roots. Our findings support the hypothesis regarding the importance of DSE at high altitudes and suggest a functional relationship between the rate of DSE/AMF and proportion of fine roots. The colonization by the root pathogen Olpidium sp. in C. quinoa deserves further study since this Andean grain is increasingly important for the local economy in these marginal areas.