A two-sludge system consisting of anaerobic anoxic oxic biological contact oxidation (A(2)/O BCO) was developed to treat domestic wastewater with a low carbon/nitrogen (COD/TN) ratio (around 3.21) by shortening sludge retention time (SRT) for phosphorus accumulating organisms (PAOs) in the A(2)/O reactor and prolonging SRT for nitrifiers in the BCO reactor. Specifically, the BCO reactor was composed of three stages in series (N-1, N-2 and N-3), so that simultaneous nitrogen and phosphorus removals by denitrifying PAOs (DNPAOs) was achieved in the A(2)/O reactor with NO. N as the electron acceptor from the BCO reactor. Long term operational tests (600 days) were conducted with various operational parameters [e.g., hydraulic retention time (HRTs), nitrate recycling ratio (Rs), volume ratio (Vs)] to examine the denitrifying phosphorus removal performance. The system exhibited the highest removal of TN and PO43--P at the HRTs of 8 h, Rs of 300% and Vs of 2:4:1. The optimal IN and PO43--P removals were 80.30% and 96.61% at low COD/TN of 3.21. The species diversity and microbial community examined by the Illumina MiSeq method demonstrated the fact of two sludge system, and the improved community structure by long-term optimization was prominent comparing with the seed sludge. Additionally, Accumulibacter and Dechloromonas were the dominant functional PAOs with 25.74% in the A(2)/O reactor, while nitrifiers (including Nitrosomonas and Nitrospira) were gradually enriched with 13.10%, 21.33%, and 31.10% in the three stages of the BCO reactor. (C) 2016, The Society for Biotechnology, Japan. All rights reserved.