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Aims Soil fungal communities play a critical role in ecosystem carbon (C) and nitrogen (N) cycling. Although the effect of plant invasions on ecosystem C and N cycling is well established, its impact on soil fungal communities is not fully understood. The objective of this study was therefore to understand the variations in soil fungal communities as affected by plant invasion, and the mechanisms that drive these changes. Methods We examined the impacts of invasive Spartina alternifolia Loisel. (SA) on soil fungal abundance, diversity, community composition, trophic modes and functional groups in comparison with bare flat (BF) and native Suaeda salsa (Linn.) Pall. (SS), Scirpus mariqueter Tang et Wang (SM), and Phragmites australis (Cav.) Trin. ex Steud. (PA) communities in coastal salt marshes of eastern China, based on analyses of the quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequences of fungal internal transcribed spacer (ITS) region. Results SA invasion increased the soil fungal abundance and diversity compared to BF, SS, SM, and PA soils. The increased soil fungal abundance and diversity were highly related to soil organic carbon (C) and nitrogen (N), water-soluble organic carbon (WSOC), litter C:N ratio, and root C:N ratio. Soil fungal community composition was shifted following SA invasion. Specifically, SA invasion significantly enhanced the relative abundance of Basidiomycota, and reduced the relative abundance of Ascomycota compared with BF, SS, SM, and PA soils. Additionally, SA invasion changed soil fungal trophic modes and functional groups. The relative abundance of saprotrophic fungi significantly increased, while the relative abundances of symbiotic and pathotrophic fungi decreased following SA invasion. Conclusions Our data revealed that SA invasion altered soil fungal abundance, diversity, community composition, trophic modes and functional groups, which were primarily driven by the quality and quantity of plant residues, soil nutrition substrates, as well as soil physicochemical properties. The changes in soil fungal communities, especially their trophic modes and functional groups following SA invasion would greatly affect soil C and N decomposition and accumulation with potential feedback on climate change.