Abstract: To furth er u nderstand the microbial structure and niche characteristics of sediment in the ponds planted with Myriophyllum elatinoides, high-throughput sequencing technology was used in this study to analyze the structure of bacteria and niche characteristics of dominant bacteria from the composition of bacteria at the level of phylum and genus. Niche width of dominant genera and niche overlap index were calculated, and the relationship between dominant genera and environmental physicochemical factors was analyzed in this paper. The results showed that the bacteria in the sediment of fishpond planted with Myriophyllum elatinoides belong to 63 phyla, 153 classes, 190 orders, 168 families and 143 genera, and 15 dominant generas of bacteria of 6 phyla mainly concentrated in Proteobacteria, followed by Chloroflexi, Bacteroidetes, Acidobacteria, Nitrospira and OP8 etc.The niche width of 15 dominant genera ranged from 0.584 to 0.957, 80% of which was larger than 0.8. The range of niche overlap value of dominant genera was 0.505～0.983, and those with niche overlap value greater than 0.6 accounted for 98.0% of the total logarithm of dominant genera. Niche breadth and overlap value showed that the resource utilization and survival ability of the dominant genera were strong. There was fierce resource competition,and the spatial heterogeneity was small. The redundancy analysis result showed that the concentrations of TP,Ammonia and OM were the main environmental factors, which affected the abundance of dominant bacteria. The results of this study provided a scientific basis for revealing the effects of Myriophyllum elatinoides on the environmental microorganisms in freshwater aquaculture ponds.