A full-scale biosystem consisting of two anaerobic reactors (HA and BF1) and four aerobic ones (BF2-BF4 and OD) in succession and receiving antibiotic-bearing (mainly streptomycin) wastewater was used for studying the impacts of antibiotics on microbial community structures. Significant decreases of streptomycin (from 3955 ± 1910 to 23.1 ± 4.7 μg L(-1)) and COD(Cr) were observed along the treatment process. Cloning results show that the anaerobic reactors (HA and BF1) were dominated with Deltaproteobacteria (51%) mainly affiliated with sulfate-reducing bacteria (SRB), while the aerobic BF2 receiving streptomycin of 408.6 ± 59.7 μg L(-1) was dominated with Betaproteobacteria (34%), Deltaproteobacteria (31%) and Bacteroidetes (14%). Gammaproteobacteria (15.9-22.4%), Betaproteobacteria (10.0-20.3%), and Bacteroidetes (4.5-29.7%) became the major bacterial groups in aerobic BF3-OD receiving streptomycin of ≤83 ± 13 μg L(-1). Archaea affiliated with Methanomethylovorans hollandica-like methylotroph was abundant in HA and BF1 (archaea/bacteria, 0.54-0.40; based on specific gene copy number), suggesting the coexistence of SRB and methanogens in degrading pollutants. Fungi were abundant (fungi/bacteria, 0.15; based on specific gene copy number) with the dominance of Ascomycota (clone ratio of Ascomycota/eukarya, 25.5%) in BF2, suggesting that fungi could be an important player in pollutant removal under high levels of antibiotics. This study demonstrates that under high antibiotic levels, wastewater treatment communities may maintain system stability through adjusting bacterial, archaeal, and eukaryal compositions.