We assessed the diversity and distribution of soil fungal communities associated with biological soil crusts (BSCs) in the southeastern Tengger Desert (China) using 454 pyrosequencing. Soil fungal communities showed high diversity, with 63,427 reads belonging to 478 operational taxonomic units (OTUs). Of these OTUs, 369 belonged to the Ascomycota, 73 to the Basidiomycota, 24 to the Chytridiomycota, one to the Glomeromycota, five to the Mortierellomycotina, and six to unassigned phyla. The most frequent genera were Phoma, Fusarium, Alternaria, Dendryphion, Peyronellaea, Curvularia, Epicoccum, Embellisia and Pleiochaeta. Different BSC sands (algae-crust sand, moss-crust sand and lichen-crust sand) did not harbor significantly different fungal communities. However, the fungal communities in these BSC sands were significantly different from those in non-crusted sands, with members of the Hypocreales and Fusarium being more frequent in the latter. The distribution of soil fungi (measured by Bray-Curtis distance) correlated with abiotic parameters, including total P (r2 = 0.9191, P = 0.001), organic C (r2 = 0.7237, P = 0.004), total N (r2 = 0.7200, P = 0.004), pH (r2 = 0.6858, P = 0.002) and electrical conductivity (r2 = 0.4723, P = 0.030). The results suggest that BSCs in the Tengger Desert harbor diverse fungal communities that are influenced by abiotic factors. Keywords: Biological soil crust; Desert environments; Environmental factors; Fungal community.