Abstract:[Objective] To study the prokaryotic and eukaryotic community structure and the physicochemical factors influencing their distribution in three mine wastewater lakes from a pyrite mine in Anhui Province. [Methods] Geochemical analysis characteristics of three wastewater lakes were measured, and microbial community compositions of the lakes were studied using high-throughput sequencing. The relationship between microbial community structure and environmental factors was also analyzed based on statistical methods. [Results] Samples from three wastewater lakes included two acidic and one neutral, with significant differences in physicochemical properties. Lake TF, typically acidic, formed about 5 years ago and is characterized by low pH (2.55±0.01), Fe (154.95±0.78 mg/L) and SO42- (3374.86±3.81 mg/L). Lake PT is also acidic, pH (2.9±0.02), however, it formed in the 1970's, and has significantly lower Fe (34.57±4.00 mg/L) and higher SO42- (10398.98±626.70 mg/L) than lake TF. Lake DS is neutral (freshwater), characterized by pH (7.55), high content of SO42- (4162.99 mg/L), while other main metal ions detected were Mg (594.90 mg/L) and Ca (650.10 mg/L). It was observed that the prokaryotic biodiversity of the three wastewater lakes generally increased with increasing pH. The prokaryotic composition of the two acidic wastewater lakes was relatively close. However, lake TF was dominated by autotrophic iron oxidizing bacteria (69.54%±2.89%), while lake PT by heterotrophic bacteria (64.45%±13.81%). The ratio of autotrophic iron oxidizing bacteria Ferrovum in TF was (64.17±1.84)%, and it decreased to (35.39±13.74)% in PT. However, heterotrophic bacteria were abundant in PT as observed by the distribution of Acidicapsa (15.75%±3.99%), Acidiphilium (10.65%±2.05%), and Acidisphaera (6.34%±1.02%). Lake DS had a typically distinct microbial community compared to acid lakes (TF and PT) despite of a high content SO42-. Lake DS had an abundance of Limnohabitans (18.47%) and Rhodobacter (8.42%). The eukaryotic community of three wastewater lakes was mainly composed of algae. The acidic lakes (TF and PT) were mainly populated by Ochromonas and Coccomyxa, accounting for (53.65%±2.02%) in TF and (68.84%±10.4%) in PT respectively. Lake DS was mainly characterized by Cyclotella (49.85%). From our analyses of physicochemical factors, we found that pH was the main factor affecting microbial community composition in acidic wastewater lakes.