Microbial fungi and bacteria are ubiquitous, occurring in highly enriched concentrations in biological soil crusts (biocrusts), as compared to the surrounding uncrusted soil. Nevertheless, their diversity can hardly be estimated without molecular biology methods. Only the macroscopic phenotypes of lichen-forming fungal species, which may dominate the landscape in soil crust habitats, allow a more or less secure determination to species level even in the field. Lichens in biocrusts have therefore long been studied (see Chap. 1 by Lange and Belnap) and their diversity and ecosystem services specifically addressed in Chap. 7 by Rosentreter et al. Knowledge on the diversity of non-lichenized fungi in biocrusts is still quite limited, whereas investigation of bacterial communities has received global attention in the past decade. This chapter aims to review the current state of research on bacterial and fungal community composition in biocrusts.