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Plant invasions severely threaten the stability and biodiversity of fragile ecosystems in karst areas. Elucidating the microbial mechanisms underlying the interactions between invasive plants and native plants in rhizosphere soil is crucial for preventing plant invasions. In this study, high-throughput sequencing was used to compare the differences in rhizosphere fungi between two invasive and native plants in the Guizhou karst region. These findings provide theoretical support for understanding the ecological impact of invasive plants and for developing ecological management strategies based on soil microorganisms. The results revealed the following: (1) A total of 16 soil samples were included in the study, which comprised 1 phylum, 50 classes, 112 orders, 245 families, 463 genera and 629 species. (2) No significant differences were observed in the Ace, Chao, Shannon, Simpson and Sobs indices of the rhizosphere fungal communities between invasive plants and native plants (p > 0.05). (3) At the phylum level, no significant difference was observed in the community compositions of invasive and native plants; the dominant phyla were Ascomycota, Mortierellomycota and Basidiomycota; at the genus level, there were significant differences in the community composition of invasive and native plants, and the relative abundances of Minimedusa, Monocillium and Gymnopus in the rhizosphere soil of invasive plants were significantly higher (p < 0.05). (4) Functional predictions based on FUNGuild indicated a higher relative abundance of saprotrophic fungi associated with invasive plants. Community assembly processes for both invasive and native plants were primarily governed by stochastic ecological processes (e.g., drift). These findings suggest that plant invasion is associated with shifts in the composition and potential ecological functions of rhizosphere fungal communities in the karst area.