To characterize the effects of pentachlorophenol (PCP) on the performance and microbial community of aerobic granular sludge in sequencing batch reactor (SBR), the web-based terminal restriction fragment length polymorphism (T-RFLP) and real-time PCR (RT-PCR) techniques were used to explore the bacterial community structure. When PCP increased from 0 to 50 mg/L, the COD removal rate changed little, while the ammonia removal rate dropped from 100% to 64.9%. The results of molecular characterization showed that the quantity of ammonia oxidizing bacteria (AOB) kept constantly, although the number of bacteria species decreased with the increase of PCP concentration. Significant shift in bacterial community structure at different PCP stresses was observed within aerobic granular sludge. When the PCP was absent, there are 69 strains in aerobic granular sludge detected by T-RFLP method. With the increase of PCP, most of bacteria disappeared and only 19 bacteria existed at all five PCP concentrations. These results contributed to comprehensive understanding of the microbial community structure under the PCP stress and its relationship with the performance for wastewater treatment by aerobic granular sludge.