Molecular methodologies were used to investigate free-living fungal communities associated with biological soil crusts (BSCs), along km-scale transects on the Colorado Plateau (USA). Two cyanobacteria-dominated crust types that did not contain significant lichen cover were examined. Fungal community diversity and composition were assessed with PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and sequencing, and fungi-specific quantitative PCR was used to measure fungal population densities as compared with those of bacteria. Our results clearly indicate that free-living fungi, while ubiquitous in BSCs, are less diverse and contribute far less biomass than their bacterial counterparts. Biological soil crust fungal community [...]