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The purpose of this study is to assess the application of denaturing gradient gel electrophoresis (DGGE) for analyzing the bacterial and cyanobacterial diversities of biological soil crusts (BSCs) in sandy land. Soil microbial DNA was extracted from BSCs under different plantations in Horqin Sandy Land of Northeast China. 16S rRNA gene fragments from bacteria and cyanobacteria were amplified by universal bacterial and cyanobacteria-specific primers. Fourteen and six prominent bands were detected in the bacterial and cyanobacterial DGGE profiles, respectively. These bands were excised, cloned and sequenced. Phylogenetic analysis classified the bacterial sequences into the following main groups: Escherichia, Bacillus, Paenibacillus, Shigella, and Pseudomonas. The cyanobacterial sequences were classified as Microcoleus, Leptolyngbya and Haslea. Our study suggests that DGGE is a useful technique for detecting dominant species compositions of bacterial and cyanobacterial communities in biological soil crusts, and specific primers are recommended for PCR of 16S rRNA gene fragments.