Soil microorganisms play key roles in soils through regulating organic matter decomposition and plant nutrient availability. However, due to the complexity of microorganism survival condition, only 1%-5% of the total microorganisms can be isolated by cultural method in soils. Recently, the advances of molecular biological techniques can provide information regarding soil bacterial community structure through culture-independent approaches. To better understand the impact of grassland degradation on the composition and structure of soil bacterial community, the total DNA of microorganisms was extracted directly and amplified by the 16S rRNA gene specific primers of f954 with GC clamp and 1369r, and the changes of the soil bacterial community structure in degraded area (including light, moderate and heavy degraded) of desert steppe ecosystem in Inner Mongolia were determined by the PCR-DGGE method. Results indicate that soil bacterial community structures in degraded desert steppe changed significantly. In 2006 summer，Shannon-Weaver Indices decreased as increasing of degradation degree, ie., the highest in the light degradation area, followed with moderate degraded area, and the least in heavy degradation area. In 2007 summer, they decreased initially and then increased, ie., in the light, heavy and moderate degradation areas, they decreased orderly. Seventeen 16S rDNA clones were sequenced and their accession numbers in the data bank were EU327142-EU327157 and EU327164. Compared with deposited in the Genbank (www.ncbi.nlm.nih.gov), it shows that their level of nucleotide identity changed with a range from 95 to 100%. The phylogenetic affiliation of bacteria determined by 16S rDNA sequencing of cloned DNA fragments in different degraded desert steppe indicate that they were mainly attributed to Bacteroidetes, Acidobacteria, γ、δ groups of Proteobacteria and Firmicutes and in which Bacteroidetes were dominant with 47%.