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The Qaidam Basin is the most extensive (120 000 km2) basin on the Qinghai–Tibet Plataea (QTP). Recent studies have shown that environmental selection and dispersal limitation influence the soil fungal community significantly in a large-scale distance. However, less is known about large-scale soil fungal community assemblages and its response to the elevation gradient in the high-elevation basin ecosystems. We studied fungal assemblages using Illumina sequencing of the ITS1 region from 35 sites of the Qaidam Basin. As the increase of elevation, fungal species richness and Chao1 index also increased. The Ascomycota was the most abundant phylum (more than 70% of total sequences), and six of the 10 most abundance fungal family was detected in all 35 soil samples. The key factors influencing the soil fungal community composition in the Qaidam Basin were environmental filtering (soil properties and climate factors). The Mantel test showed no significant relationship between geographic distance and community similarity (r = 0.05; p = 0.81). The absence of the distance effect might be caused by lacking dispersal limitation for the soil fungal community.

Environmental filtering affects fungal communities more than dispersal limitation in a high-elevation hyperarid basin on Qinghai–Tibet Plateau