The bacterial communities under different redox conditions of an integrated anoxic-aerobic membrane bioreactor (AO-MBR) were studied to profile the bacteria responsible for biodegradation/biotransformation of the contaminants and to uncover the influence of internal sludge recirculation on the community structure. The lab-scale AO-MBR achieved high and stable removal for organic, nutrient and trace organic contaminants over a 6-month experimental period. Sludge DNA samples were subjected to amplification of 16S rRNA genes followed by 454 pyrosequencing. With 5248 and 5721 high quality sequences obtained, 555 and 614 operational taxonomic units (OTUs) at 3% cut-off level were assigned for bacterial communities under aerobic and anoxic conditions, respectively. The unique OTUs under these two conditions were 340 (aerobic) and 399 (anoxic), together accounting for 77% of the total observed. However, the rest 23% shared between both communities cover the majority of sequence reads (85% and 83% for anoxic and aerobic communities, respectively). They predominated the system and were high in functional organization (Fo ≈ 0.78). Proteobacteria, Bacteroidetes and Plantomycetes topped the abundance list of all bacterial phyla identified. Their relative abundance was very similar between the two communities. In addition, this study also identified functionally bacterial groups for nutrient removal including Nitrospira (nitrite oxidizing bacteria), Nitrosomodaceae (ammonia oxidizing bacteria), Gemmata & Pirellula (ANAMMOX bacteria) and the polyphosphate-accumulating organisms such as Candidatus Accumulibacter. In conclusion, the differences in operating condition and functionality of aerobic and anoxic reactors during treatment process of AO-MBR can sustain two different bacterial communities in which the varieties of bacteria were mostly unique. However, the majority of bacteria were found existing in both communities. Possibly, the condition formed under high sludge recirculation between two reactors flourish the growth of shared bacterial community that are responsible for the main function during treatment process of this combined MBR system.