The alkaline phosphatase encoded by phoD gene drives the mineralization of organic phosphorus in sediments and thus the release of bioavailable phosphorus, and promotes the growth and blooms of cyanobacteria in eutrophic lakes. The dynamic variations of phoD-harboring bacterial community during the annual cyanobacterial growth and decline in eutrophic lakes, however, remain unclear. In this study, we analyzed the alkaline phosphatase activity (APA), phoD-harboring bacterial community diversity and structure and their associations with the physicochemical factors in a typical eutrophic lake (Lake Chaohu) in China during the entire cyanobacterial growth and decline. The results showed that the APA in sediments increased significantly during the initial growth and outbreaks of cyanobacteria. Pseudonocardia and Friedmanniella are the predominant phoD-harboring genera in sediments during the entire cyanobacterial growth and decline. In contrast to the abundance of Pseudonocardia and Friedmanniella in the incubation and decline stages of cyanobacteria, Pseudonocardia decreased significantly while Friedmanniella increased significantly in the early growth and outbreak stages. The abundance of phoD gene bacteria varies spatiotemporally, especially for its high spatial heterogeneity. The Ace and Shannon diversity index of phoD-harboring bacterial community during the early and outbreak stages of cyanobacteria were much higher than those in the incubation and decline stages. The changes of phoD-harboring bacterial community were mainly driven by APA, dissolved oxygen, chlorophyll-a, water temperature, total phosphorus and inorganic phosphorus. The rapid decline of dissolved inorganic phosphorus in overlying waters due to the increasing cyanobacterial photosynthesis in the early growth of cyanobacteria induces the APA, promotes the growth of Friedmanniella and alleviates the phosphorus restriction.