•Higher diversity of bacteria was found in high concentration swine wastewater.•Bacterial diversity was strongly positive correlation with DO.•Bacterial community distribution was strongly positive correlations with N and P.•Proteobacteria played an indispensable roles in M. elatinoides purification system.•Bacterial community dynamics was responsive to swine wastewater treating process. Constructed wetlands are important ecological tools for treating municipal, industrial, and agricultural wastewater. Terminal restriction fragment length polymorphisms and clone libraries were employed to determine the variation in bacterial community diversity and structure from a Myriophyllum elatinoides purification system used to treat different concentrations of swine wastewater. Experiments included tap water (control), a low concentration of swine wastewater (S1, 200ppm NH4+), and a high concentration of swine wastewater (S2, 400ppm NH4+) in small tanks. The total nitrogen (TN) and total phosphorus (TP) removal efficiency were equal to or greater than 93.9% and 93.1%, respectively, in 28d. Higher diversity of bacteria was found in S2 on day 7 and day 14. In total, 221 genera representing 17 phyla were detected. Acidobacteria and Proteobacteria dominated at the phylum level in sediments, with relative abundance ranging from 33.3% to 50% and 26.2 to 42.9%, respectively. Proteobacteria was primarily represented by Betaproteobacteria and Deltaproteobacteria at the class level on days 7, 14, and 28, and Nitrospira was detected on day 7. Verrucomicrobia was positively related to NH4+ (Pearson’s correlation, P<0.05), Bacteroidetes was negatively related to NH4+ (P<0.05). Redundancy analysis revealed that the bacterial community distribution was strongly positively correlated with TN, ammonia, TP, and phosphate in S1 and S2, these environmental parameters had a much stronger effect on S2 than S1. However, the bacterial diversity was strongly positively correlated with dissolved oxygen (P<0.01). Certain bacteria were implicated in nitrogen and phosphorus removal in the M. elatinoides purification system, and the bacterial community dynamics changed as the environmental factors were altered during purification, therefore, wastewater parameters could predict the microbial community structure. Our results reveal microbial N and P removal process, which are important for M. elatinoides purification system studies in the field.