The bacterial diversity of an antibiotic industrial wastewater treatment system was analyzed to provide the information required for further optimization of this process and for identification of bacterial strains that perform improved degradation of antibiotic industrial wastewater. The total bacterial DNA of samples collected at three stages (aeration, precipitation, and idle) during the sequencing batch reactor (SBR) process were analyzed by polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) of the 16 s rDNA V3 regions. Community analysis was conducted in terms of the richness value (S), the dominance degree and the Shannon–Wiener diversity index (H). Rich bacterial diversity was apparent in the aeration stage of the SBR process, and the number of bands in the aeration stage was more abundant than that in the precipitation and idle stages. The DGGE analysis showed 15 bands, six of which were uncultured bacteria, and included one anaerobic and five aerobic bacteria. The microbial community in the aeration stage was the most complex of the whole SBR process, while the dominant bacteria differed in each reaction stage. These results demonstrate the cyclical dynamic changes in the bacterial population during the SBR process for the treatment of antibiotic industrial wastewater.