The cessation of mowing in subalpine grasslands promotes the dominance of Festuca paniculata leading to the reduction in plant diversity. Moreover, it affects positively the abundance of Epichloe sp. inhabiting F paniculata leaves and negatively the soil density of arbuscular mycorrhizal fungi (AMF). We explored how the cessation of mowing influences root AMF communities in F. paniculata and the neighboring plants, and Epichloe sp alkaloids. Thirteen AMF operational taxonomical units were found. The neighboring plants affected positively the abundances of Aalpin and GLOM_7 whereas the interaction plant/management type influenced significantly Claroide_1, GLOM_1 and GLOM_7. The N-formylnorloline, produced by Epichloe sp. increased in unmown grassland. Hence, the cessation of mowing, coinciding with the high abundance of endophyte alkaloid, affected root-associated AMF with differential responses at the abundance level. The N-formylnorloline could be one compound underpinning the dynamic of plant diversity with a resulting structuration of AMF in subalpine grasslands.