The startup and long term operation of enhanced biological phosphorus removal (EBPR) in a continuous-flow reactor (CFR) with granules were investigated in this study. Through reducing the settling time from 9 min to 3 min gradually, the startup of EBPR in a CFR with granules was successfully realized in 16 days. Under continuous-flow operation, the granules with good phosphorus and COD removal performance were stably operated for more than 6 months. And the granules were characterized with particle size of around 960 mu m, loose structure and good settling ability. During the startup phase, polysaccharides (PS) was secreted excessively by microorganisms to resist the influence from the variation of operational mode. Results of relative quantitative PCR indicated that granules dominated by polyphosphateaccumulating organisms (PAOs) were easier accumulated in the CFR because more excellent settling ability was needed in the system. (C) 2016 Elsevier Ltd. All rights reserved.