High-elevation ecosystems are at risk of disruption from the future effects of climate change. Sub-alpine meadows are a source of unique plant populations, intraspecific variation of elevationally extreme populations, and vital sources of fresh water resources. We evaluated the whole fungal communities, arbuscular mycorrhizal fungal (AMF) communities, plant communities, and edaphic variables of sub-alpine meadows in undisturbed, disturbed, and disturbed with a non-native member of the Brassicaceae (Thlaspi arvense) plots. In conjunction with measuring the effects of disturbance on native communities we conducted potting experiments on a dominant grass of sub-alpine meadows (Festuca thurberi). We also surveyed T. arvense with 14 other members of the Brassicaceae for association with AMF in the context of a broad review of the literature for instances of Brassicaceae members found with arbuscules in their fine roots. We found that T. arvense disrupts native fungal and plant community dynamics by filtering phylogenetic diversity of AMF. In addition, we determined that intraspecific variation in F. thurberi is greater than variations in treatments associated with synthetic invasion. Several members of the Brassicaceae were also found to have arbuscules present in fine roots that may be relevant to AMF biogeography.