A submerged membrane bioreactor (SMBR) and a conventional activated sludge system (CAS) were compared in parallel over a period of 210 days on treating synthetic ammonia-bearing inorganic wastewater under similar conditions. Except for a short period of pH control failure, almost complete conversion of NH(4)(+)?N to NO(3)(-)?N was constantly achieved over an NH(4)(+)?N concentration range from 180 to 1300mgl(-1) at a hydraulic retention time (HRT) of 24h in the SMBR, compared to an average conversion ratio of 95.0% in the CAS. Scanning electron micrographs (SEMs) demonstrated the accumulation of extracellular polymeric substances (EPSs) in the SMBR. Ubiquinone-8 (UQ-8), followed by UQ-10, UQ-7 and UQ-9, was the dominant ubiquinone in both the systems. The dominant menaquinone in the SMBR was menaquinone-6 (MK-6), while that in the CAS was MK-7, indicating that some differences existed between the two systems in terms of microbial community structure. Soluble microbial products (SMPs) tended to accumulate, and then biodegrade in SMBR.