Wetland soil bacterial community structure was studied through 16S rDNA gene. The soil samples were collected from the three different ecological types of Deyeuxia angustifolia in the Sanjiang Plain field experiment station of the institute of natural ecology, Heilongjiang Academy Sciences. Total microbial DNA was directly extracted from three soil samples, and the 16S rDNA genes were sequenced and analyzed by Miseq molecular technology. The results showed that the bacterial community composition was changed significantly, both Shannon index and Chao’s index decreased indicating bacterial diversity was decreased with increase in soil moisture content. Acidobacteria was predominated both in meadow wetland and paludification meadows wetland, followed by Proteobacteria . The Proteobacteria was predominated in paludification wetland, followed by Acidobacteria . The distribution of Acidobacteria was decreased and Proteobacteria increased with increasing soil moisture content. The heatmap tree based on the 16S rDNA sequences showed that wetland water level affected the structure of Acidobacteria and Proteobacteria greatly.