Abstract:[Background] Acid mine drainage should be treated before discharge. After treatment, its physicochemical properties will be changed significantly, which would affect the whole microbial community structure. [Objective] The changes of bacterial and fungal communities before and after treatment and their relationships with physicochemical parameters were analyzed to provide reference indexes for the treatment of acid mine drainage and theoretical basis for the remediation of mine-contaminated sites. [Methods] Acid mine drainage in Zijinshan copper mine, Fujian province was collected, followed by analysis of physicochemical properties. The microbial community structures of water samples were analyzed by high-throughput sequencing technology based on 16S rRNA gene V4 region of prokaryotes and 18S rRNA gene ITS sequences of fungi. [Results] Compared with the pit water and leachate from the dump-leaching, the back water showed a higher pH and a lower content of heavy metal ions after the neutralization treatment. The diversity of prokaryotes was higher than that of fungi in all samples, and the microbial diversity of back water was higher than that of pit water and leachate. Proteobacteria was the most abundant lineage in the back water, and Euryarchaeota and Nitrospirae were of the highest abundance in the pit water and the leachate, respectively. At the genus level, Hydrogenophaga in the back water was the dominant group, while Leptospirillum was the dominant bacterium in the pit water and leachate, and archaea such as Ferroplasma also accounted for a considerable proportion. The pH, Al, Mn and Zn were significantly correlated with the genera with high relative abundance in the back water, while the high-abundance groups in the pit water and leachate had no significant correlation with the environmental factors. [Conclusion] The study indicated that the neutralization and precipitation treatment of acid mine drainage imposes a great impact on the microbial community, and the changes in microbial community structure could be used as a reference index for acid mine drainage pollution treatment efficiency.