Abstract An anoxic/aerobic membrane bioreactor treating sulfamethoxazole (SMX) and tetracycline hydrochloride (TC) containing wastewater was used for examining impacts of antibiotics on microbial communities. Results showed that 100 μg·L −1 SMX and 100 μg·L −1 TC hardly affected the pollutant removals. SMX and TC dosage up to 2000 μg·L −1 triggered a significant nitrate accumulation (i.e. TN removals decreased) while COD and ammonia removals remained stable. Along the increasing antibiotic additions, typical aerobic heterotrophic bacteria and autotrophic nitrifying bacteria remained at high abundance of 40% and 7% respectively, while the relative abundance of representative and potential denitrifying bacteria decreased by 86% at 1000 μg·L −1 SMX and 1000 μg·L −1 TC addition. Our findings elucidate that denitrification is more vulnerable than nitrification and carbon oxidization processes under antibiotic stress. Redundancy analysis also revealed that microbial communities may maintain system stability through gradual acclimation of functional bacteria and development of potential antibiotic resistance species.