Southern Chilean pristine temperate rainforests have been floristically stable during the Holocene, thus representing a pre-industrial baseline of forest ecology. Given this and its edaphic limitations, it is imperative to better understand these forests ecological patterns of mycorrhizal symbiosis. Therefore, here we compare the arbuscular mycorrhizal (AM) communities in three treeline Nothofagus pumilio contrasting plots of Chilean Andes (a volcano crater, pristine forest, and disturbed forest). The AM community assemblages were determined by morphological identification and spore counting, in three A horizon soil samples by plot. In the same nine soil samples, standard chemical analysis was performed. Eighteen AM species were described; Acaulospora was the most abundant genus. The forest plot had the highest AM species richness compared to the disturbed and crater plots. Interestingly, soils Olsen P (plant available phosphorus), pH, and Al+++ saturation similarly affected the AM assemblages. We suggest that some AM species could be specially adapted to extremely high Al saturation and extremely low plant available P conditions, as those experienced on Andean Nothofagus forests. These species may help initiate biological succession on highly disturbed ecosystems. We suggest that mycorrhizal fungi play a key role in seedling colonization of extreme environments such as the Andean treeline.