In this study, the impacts of ZnO Nanoparticles (NPs) on the microbial community in enhanced biological phosphorus removal (EBPR) system and its recoverability were investigated. High-throughput sequencing was applied to study the microbial community shift. Results show that the species richness in the EBPR system was reduced under the condition of ZnO NPs with high concentration (above 6 mg/L). Evolution analysis suggests that higher concentration ZnO NPs induced more microbial community shift. According to the analysis on genus level, Competibacter was more impressionable than Accumulibacter after exposure to 2 mg/L ZnO NPs. Nonetheless, this phenomenon could not be found as the concentration of ZnO NPs got higher (above 6 mg/L). Accumulibacter could reach to the initial level after recover for 20 days, whereas Competibacter could not recover even when the concentration of ZnO NPs was only 2 mg/L. Interestingly, although the phosphorus removal (P-removal) process was re-achieved, the microbial community in reactors was irreversible. (C) 2016 Elsevier Ltd. All rights reserved.