The occurrence and fate of antibiotics in biological wastewater treatment facilities have given rise to significant concerns. This study assessed the effects of fluoroquinolones (FQs), one class of representative antibiotics in wastewater, on the performance and the bacterial community of an anoxic-aerobic membrane bioreactor operated for one year. Results show that addition of FQs to feed wastewater caused significant increases of chemical oxygen demand (COD) in the mixed liquor. Nitrogen species in permeate increased slightly after the addition of FQs but then decreased to steady levels after long-term adaptation. However, phosphorous removal was consistently poor after FQs addition. 16S rRNA gene-targeted 454-pyrosequencing revealed a sharp decrease in the microbial species richness after FQs addition and significant fluctuations of bacterial community structure at both phylum and genus levels. Members of the two dominant phyla (Proteobacteria and Bacteroidetes) appeared to be well-adapted to the FQs. Moreover, changes in relative abundance of genera (e.g., Nitrospira, Dechloromonas, Acidovorax and Opitutus) involved in nitrogen cycling were in agreement with the reactor performance of nitrification and denitrification. Clone library analysis of the amoA gene further revealed a drastic shift of dominant ammonia-oxidizing bacteria (AOB) from the Nitrosomonas communis lineage (before FQs addition) to the Nitrosomonas oligotropha lineage (after FQs addition). Batch tests on the nutrient removal and FQs biodegradation further supported the changes in microbial community structure. This study provides a much-needed look at the bacterial community dynamics in activated sludge bioreactors for the treatment of antibiotics-containing wastewater. (C) 2015 Elsevier B.V. All rights reserved.