The symbiosis between land plants and arbuscular mycorrhizal fungi (AMF) is one of the most widespread and ancient mutualisms on the planet. However, relatively little is known about the evolution of these symbiotic plant–fungal interactions in natural communities. In this study, we investigated the symbiotic AMF communities of populations of the native plant species Pilea pumila (Urticaceae) with varying histories of coexistence with a nonmycorrhizal invasive species, Alliaria petiolata (Brassicaceae), known to affect mycorrhizal communities. We found that native populations of P. pumila with a long history of coexistence with the invasive species developed more diverse symbiotic AMF communities. This effect was strongest when A. petiolata plants were actively growing with the natives, and in soils with the longest history of A. petiolata growth. These results suggest that despite the ancient and widespread nature of the plant–AMF symbiosis, the plant traits responsible for symbiotic preferences can, nevertheless, evolve rapidly in response to environmental changes.