Constructed wetlands are efficient and economic sewage disposal means, characterized by stimulation of natural wetland ecosystems. They could remove the pollutants of wastewater to achieve purification of sewage, and microbes play an important role in this process. The aim of this study is to investigate bacterial community structure variation after effective wastewater treatment with constructed wetlands. We collected the water samples from the outfall of paper mill and outlet of constructed wetlands, and examined several parameters of the conventional water quality. Using DGGE method and cloning sequencing analysis of dominant microbes, we analyzed the variation of the bacterial community structure and major microbial species in the water samples. The results are as follows: (1)The water quality was greatly improved after papermaking wastewater treatment with constructed wetlands; (2) The structure of bacterial community remarkably changed, showing that the major microbes in the wastewater changed from Gamma-proteobacteria and Chlamydia to Alpha-proteobacteria, with the decrease in the Shannon-wiener's index; (3)Before papermaking wastewater treatment, dominant pathogenic bacteria included Legionella, Klebsiella and Parachlamydia and degrading bacteria included Thioalkalivibrio, Dehalococcoides and Hyphomicrobium. In contrast, the main priority of microbes became environment friendly bacteria such as Mesorhizobium and Rhizobium mostly, and the species and proportion of pathogenic bacteria significantly decreased after treatment with constructed wetlands. These findings suggest that constructed wetlands can not only improve water quality and change the structure of microbial community, but also remove a great deal of pathogens in the wastewater, providing powerful experimental evidence for application of constructed wetlands in industrial wastewater treatment and assessment of microbial ecology safety in the future.