Abstract: The structure and function of microbial communities in aquatic ecosystems have been widely reported. In eutrophic waters, bacteria play an important role in the occurrence, development, decline and degradation of Microcystis blooms. In this paper, we described the unique characteristics ofMicrocystisand bacterial communities in the water column and sediment, as well as the responses of the dynamics of Microcystis and bacterial communities to environmental factors. Furthermore, the interactions between Microcystis and bacteria were summarized from the following aspects: first, attached bacteria can mediate the growth of Microcystis in the microenvironment of algal cells. Second, bacteria are involved in the formation and maintenance of Microcystis colonies. Third, bacteria regulate the aggregation and degradation of Microcystis blooms. Fourth, the bacterial degradation of microcystins was introduced. Finally, the future research focus of the relationships betweenMicrocystisand bacteria and the available omics technology were prospected.