Effects of flue gas desulfurization gypsum by-products(FGDB) on alkaline-saline soil bacterial community structure was studied through 16S rDNA gene. Total microbial DNA was directly extracted from both treatment soils.We collected soils including those amended with FGDB(0.74 g m-2) and control treatments(CK) from 0-20 cm and 20-40 cm depths in Pingluo County, in Northwest China. The clone libraries were constructed after cloning and sequencing. The results showed that the bacterial community composition of alkaline-saline soil amended with FGDB changed significantly as compared with control treatment, both Shannon index and evenness increased which indicating the increase of bacterial diversity. We tested Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, Firmicutes,Verrucomicrobia, Gemmatimonadetes, Cyanobacteria, Bacteroidetes and the uncultured bacterial clones. The largest fractions were Actinobacteria which accounting for 36.4%, 33.8%, 24.7% and 30.1% of the total clones, respectively.Application of FGDB induced obvious increase of Proteobacteria as compared to CK. In contrast, the genotypes of Actinobacteria and Firmicutes decreased in 0-20 cm depth. The phylogenetic tree based on the 16S rDNA sequences showed that the application of FGDB changed the distribution of Proteobacteria to the greatest extent,followed by Actinobacteria and Firmicutes.