Abstract: In order to explore changes in community structure and diversity of the planktonic and sediment bacteria in the Zhushan Bay of Lake Taihu, and to investigate relationships between bacteria and environmental factors, researches were carried out on community structure and diversity of planktonic and sediment bacteria in the Zhushan Bay of Lake Taihu in winter using the technique of 16S rRNA gene high-throughput sequencing, and relationships of the top ten genera of planktonic bacteria leading in dominancy with environmental factors (pH, dissolved oxygen concentration, chlorophyll a concentration, algal density, total nitrogen concentration, total phosphorus concentration, etc) through redundancy analysis. Results show that at the phylum level, Cyanobacteria is relatively higher in relative abundance in the water and sediment, reaching 46.95% and 22.19%, respectively, while at the class level, unidentified Actinobacteria and unidentified Cyanobacteria in the water, accounting for 31.87% and 30.46%, respectively, of the total, and Chloroplast, Gammaproteobacteria and Nitrospira in the sediment, making up 14.34%, 10.97% and 9.89% of the total, respectively, and at the genus level, Microcystis is the most dominant one in the water and followed by hgcI clade, and Microcystis and unidentified Nitrospiraceae are the dominant ones in the sediment. Through the study it is found that in the surface water, the genus of Microcystis is the highest in relative abundance, which is positively related to algal density, dissolved oxygen concentration and pH.