Molecular methodologies were used to investigate fungal communities, free-living and lichenized, associated with biological soil crusts (BSCs) within arid-lands in the southwestern United States. Samples were collected along km-scale transects, and fungal community diversity and composition were assessed based on ribosomal genes, with PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and sequencing. Fungi-specific quantitative PCR was also used to measure fungal population densities and to compare them to those of bacteria. Localities on the Colorado Plateau that contained cyanobacterially dominated crusts, thought to be in the initial stages of colonization, were studied as were more developed BSCs dominated by lichens. Comparisons of diversity and density measures were made both between and within these crust types. The relationship of BSC fungal diversity and abundance to crust soil cover and the level of anthropogenic disturbance was also examined at the lichen-containing sites. Finally, fungal diversity in BSCs was assessed in a broader survey that included the Chihuahuan and Sonoran Deserts, in addition to the Colorado Plateau. The results indicate that while a considerable diversity of fungi is present within crusted soils overall, BSC fungi contribute less biomass and are less diverse than their bacterial counterparts. Fungal diversity in BSCs is negatively correlated with disturbance and positively correlated with crust cover, and also appears to be related to the degree of crust successional development. The overwhelming majority of crust fungi belong to the Ascomycota, and while BSC fungi and their diversity exhibit a patchy distribution in crusts from the millimeter- to the landscape-scale, members of the genus Alternaria are very widespread and frequently dominant.