Coupled granules are self-immobilized aggregates of microorganisms under micro aerobic conditions, which have the dissolved oxygen (DO) level of 0.6 mg.L−1. The effects of DO concentration on pentachlorophenol (PCP) reduction and its microbial community were investigated in a coupled anaerobic and aerobic reactor. Both the diversity and the dynamicity of the Eubacteria and Archaea community, which were responsible for PCP degradation, were evaluated by means of amplification by polymerase chain reaction (PCR) and separation using the denaturing gradient gel electrophoresis (DGGE) technique. The results demonstrated a major shift in the Eubacteria and Archaea community as the mixed aerobic and anaerobic seeding sludge (1:1 by volume) developed into coupled granules and finally acclimated with PCP throughout the experiment period within 60 days. The numbers of the Eubacteria population decreased from 20, 16 to 11; Shannon diversity index decreased from 2.75, 2.53 to 2.10. In contrast, the number of the Archaea population increased from 12, 14 to 18; and Shannon diversity index increased from 1.87, 1.88 to 2.43. Phylogenetic analysis based on 16SrDNA genes showed the dominance Sphingomonas, Desulfobulbus, Proteobacteria, Actinobacterium, Methanogenic and some uncultured bacteria in the PCP-degrading coupled granules. Microorganism community construction of coupled granules was also deduced.