The integrated fixed-film activated sludge membrane bioreactor (IFAS-MBR) has been developed as alternative to activated sludge-based membrane bioreactor (MBR) process. However, the characteristics of bacterial community in IFAS-MBR are still not fully understood. The objective of this study is to compare the bacterial community changes and structures between IFAS-MBR and MBR. The dominant, shared and functional species were also analyzed to characterize the bacterial communities in two MBRs. The results showed that two systems had excellent removal efficiencies of COD and NH4 +-N. The microbes in IFAS-MBR can achieve the highest diversity at shorter time, and the IFAS-MBR had a better ability to resist the shock temperature than the MBR. The clone libraries results showed that the bacterial community compositions in two MBRs were significantly different. Betaproteobacteria was the predominant group in IFAS-MBR, but Gammaproteobacteria was the main group in MBR. Bacteroidetes was the subdominant group in MBR, but it only occupied small proportion in IFAS-MBR. Moreover, 21 OTUs were shared between the bacterial community of MBR and IFAS-MBR.