This study aimed to investigate the effect of pulse aeration (on/off time 5/10 min) on the pollutants removal efficiencies and on the evolution of the denitrifying bacteria communities of a continuous flowing completely mixed activated sludge reactor. Organic matters and nitrogen removal were evaluated and the denitrifying bacteria community structure was analyzed by MiSeq sequencing technology. Results showed that the TOC removal rates were steadily above 81.6% and the NH4+-N removal rates were 92.1% +/- 0.5% when the pulse aerated activated sludge reactor was operated with the optimized pulse aeration cycle (PAC) of 5/10 min. There was no significant impact on both TOC and NH4+-N removal efficiencies, while the average TN removal rate of the pulse aerated reactor (58.4%) was significantly higher than that of the constantly aerated one (30.6%). The removal efficiencies of both organics and nitrogen were stable during the 60-day acclimation period regardless of the changing DO concentration fluctuated in pulse mode. Although the denitrifier bacterial compositions varied between the pulse aerated group and the constantly aerated group, the denitrifier community richness and diversity were similar. Boost of the TN removal was mainly due to the anoxic denitrifying environment provided by the non-aerated phase in each PAC. (C) 2018 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.