In this study, the bacterial dynamics and structure compositions in the two-stage biological process of a full-scale printing and dyeing wastewater (PDW) treatment system were traced and analyzed by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing techniques. T-RFLP analysis showed that the microbial communities experienced significant variation in the process of seed sludge adaptation to the PDW environments and were in constant evolution during the whole running period of the system, despite the constant COD and color removal effects. Pyrosequencing results indicated that the two-stage biological system harbored rather diverse bacteria, with Proteobacteria being the predominant phylum during the steady running period, although its microbial compositions differed. The first-stage aerobic tank was dominated by α-Proteobacteria (89.05% of Proteobacteria), whereas in the second-stage aerobic tank, β- and γ-Proteobacteria, besides α-Proteobacteria, were the dominant bacterial populations.