Berberine is a broad-spectrum antibiotic extensively used in personal medication. The production of berberine results in the generation of wastewater containing concentrated residual berberine. However, few related studies up to date focus on berberine removal from wastewaters. In this study, a lab-scale upflow anaerobic sludge blanket (UASB)-membrane bioreactor (MBR) process was developed for berberine removal from synthetic wastewater. The performance of the UASB-MBR system on berberine, COD and NH4+-N removal was investigated at different berberine loadings. And the effects of berberine on bacterial communities were evaluated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Results showed that, as the increase of berberine loadings, VASE performance was affected remarkably, whereas, efficient and stable performance of MBR ensured the overall removal rates of berberine, COD and NH4+-N consistently reached up to 99%, 98% and 98%, respectively. Significant shifts of bacterial community structures were detected in both UASB and MBR, especially in the initial operations. Along with the increase of berberine loadings, high antibiotic resisting species and some functional species, i.e. Acinetobacter sp., Clostridium sp., Propionibacterium sp., and Sphingomonas sp. in UASB, as well as Sphingomonas sp., Methylocystis sp., Hydrogenophaga sp. and Flavobacterium sp. in MBR were enriched in succession. (c) 2013 Elsevier B.V. All rights reserved.