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Abstract In aquatic ecosystems, both phytoplankton and bacteria play pivotal roles. Based on 16S rRNA gene sequencing, considerable research focused on phytoplankton colony attached and free-living bacteria has revealed the close relationship between them, and indicated that the entire bacterial community mediates crucial biogeochemical processes in aquatic ecosystems. However, our understanding of their distribution patterns and response to environmental factors remains poor. Besides, picocyanobacteria, which were omitted from attached bacteria analysis, were reported to be important in cyanobacterial blooms. To explore the spatiotemporal variation of the entire bacterial community with their driving environmental factors and detect the relationships among them, we collected 61 water samples spanning one year and the entire Lake Taihu regions for surveying the entire bacterial community. Our results indicated: 1) seasonal variation of the bacterial community composition was stronger than spatial variation due to the clearly seasonal variation of Microcystis , Synechococcus (pico-cyanobacteria) and other bacteria (Actinomycetales , Pirellulaceae and Sphingobacteriaceae); 2) the spatial distribution of the bacterial community showed that different phyla were dominant in different regions; 3) the bacterial co-occurrence networks varied seasonally and were dominated by Microcystis, ACK-M1, Chthoniobacteraceae, Synechococcus, Pirellulaceae and Pelagibacteraceae ; 4) phytoplankton density, chlorophyll a , water temperature and total nitrogen were the major factors that drove the spatiotemporal variation of bacterial community composition. This study revealed the seasonal succession and spatial distribution of the entire bacterial community in Lake Taihu, providing new insights into the relationship between water bloom-forming cyanobacterial species and other bacteria, and their response to environmental factors in eutrophic freshwater ecosystem. Graphical abstract Unlabelled Image Highlights • Analyzed the seasonal and spatial dynamics of the entire bacterial community composition involved in cyanobacterial blooms • Found strong seasonal but weak spatial succession in bacterial community composition due to the cyanobacterial variation • Explored the relationships among Microcystis , Synechococcus (pico-cyanobacteria) and their related bacteria • Determined the main factors that drove the spatiotemporal variation of bacterial community composition [ABSTRACT FROM AUTHOR]