As the number of non‐native invasive species in the world is increasing, there is a pressing need to understand the effects of invasive species on recipient biotic communities to improve our ability to migrate or relieve their potential negative effects on biodiversity and ecosystem functions. Plant invasions have been shown to impose great threats to aboveground biotic communities; however, invasive impacts on soil biota remain ambiguous, partially because of the paucity of studies with a large number of species across biogeographic gradients. Here, we characterized rhizosphere fungal communities of 53 native and invasive plants spanning approximately 1800 km in China, as well as eight pairs of phylogenetically related native versus invasive plants in a greenhouse experiment. The results of both field survey and greenhouse experiment showed that rhizosphere fungal composition was primarily predicted by plant phylogeny (e.g. family and species), and plant geographic origin (native vs. invasive) and abiotic factors had much smaller effects. We detected no differences in the number and relative abundance of total and family/species‐specific OTUs (i.e. overall, pathogens and mutualists) associated with these native and invasive plants on average, suggesting novel co‐evolution between native soil fungi and these invasive plants. These results suggest that non‐native plant invasions had only a weak impact on soil fungi, partially due to stronger controls of plant evolution on rhizosphere fungi and adaptation of native fungi to these invasive species. Interestingly, rhizosphere fungal composition was more variable between invasive plants than between native plants at middle latitudes, potentially creating spatial variations in plant–soil interactions and, in turn, invasion dynamics. These novel findings highlight the importance of integrating phylogenetic and biogeographical approaches to explore invasive effects on native biota.