Abstract: The effect of filamentous sludge bulking on the performance of a pilot-scale denitrification reactor with effective volume of 10 m ³ and flow rate of 300 m ³/d was investigated. The changes of bacterial community structure were analyzed by high throughput sequencing.When the reactor operated normally for 66 days, sludge bulking phenomenon was observed and sludge sedimentation performance deteriorated significantly; the SV30 rose from 30% to 85%, and the biomass in the reactor decreased, with the mixed liquid suspended solids (MLSS) decreasing from 3 300 mg/L to 1 400 mg/L. The microscopic examination found that a large number of filamentous micro-organisms extended out of the flocs, and the close bacterial micelles were destroyed, which indicated that the sludge bulking was mainly caused by filamentous bacteria. Furthermore, high-throughput sequencing confirmed the filamentous bacteria such as Thiothrix, Leptothrix and Haliscomenobacter were enriched after sludge bulking, and were changed by filamentous bacteria types and environmental factors, indicating that higher sulfide and lower DO may provided better conditions for sludge bulking. It was noted that the denitrification performance of the reactor was not affected by sludge bulking and sludge loss, which may attribute to the increase in abundance of denitrifiers such as Methyloversatilis, Hydrogenophaga and Thiothrix (29.74%, 1.69% and 3.45%, respectively). Besides, the shift of bacterial community structure might cause changes in the abundance of functional genes.