Biological soil crusts (BSC) of arid and semiarid regions of the world are recognized as one of the least explored niches occupied by fungi. Culture and molecular methodologies were used to investigate free living and symbiotic fungal communities associated with BSC at two sites; Wadi Al-Khoud (WK) and Al-Jabal Al-Akhdar (JAK) in the Sultanate of Oman. A total of 390 fungal isolates were obtained. Phylogentic analysis placed the majority of BSC fungi within the Ascomycota phylum with the dominance of Dothideomycetes class and Pleosporales order. A total of 44 different genera and 101 different species were identified dominanted by the following genera: Alternaria, Phoma, Fusarium, Cochliobolus, Ulocladium, Cladosporium and Myrothecium. The crust was characterized by dominance of melanin-containing fungi and a significant proportion of sexual Ascomycete species. Using Pyrosequencing, clear differences in phylum and class distributions were observed. The detected sequences belonged to phyla Ascomycota, Basidiomycota and Chytridiomycota. Lichinomycetes Leotiomycetes and Lecanoromycetes classes dominated in lichen crust and Eurotiomycetes dominated the shaded crust at WK and on the JAK. The diversity of BSC fungal communities appears to be linked with crust types as well as specific desert ecoregions, which may be indicative of a broader biogeography for BSC fungi.