Terminal restriction fragment length polymorphism (TRF or T-RFLP) analysis and 16S rDNA sequence analysis from clone libraries were used to examine cyanobacterial diversity in three types of predominant soil crusts in an arid grassland. Total DNA was extracted from cyanobacteria-, lichen-, or moss-dominated crusts that represent different successional stages in crust development, and which contribute different amounts of carbon and nitrogen into the ecosystem. Cyanobacterial 16S rRNA genes were amplified by PCR using cyanobacteria-specific 16S rDNA primers. Both TRF and clone sequence analyses indicated that the cyanobacterial crust type is dominated by strains of Microcoleus vaginatus, but also contains other cyanobacterial genera. In the moss crust, M. vaginatus-related sequences were also the most abundant types, together with sequences from moss chloroplasts. In contrast, sequences obtained from the lichen crust were surprisingly diverse, representing numerous genera, but including only two from M. vaginatus relatives. By obtaining clone sequence information, we were able to infer the composition of many peaks observed in TRF profiles, and all peaks predicted for clone sequences were observed in TRF analysis. This study provides the first TRF analysis of biological soil crusts and the first DNA-based comparison of cyanobacterial diversity between lichen-, cyano- and moss-dominated crusts. Results indicate that for this phylogenetic group, TRF analysis, in conjunction with limited sequence analysis, can provide accurate information about the composition and relative abundance of cyanobacterial types in soil crust communities.