Abstract:[Background] The associated bacteria have complex interactions with cyanobacteria.[Objective] To study the effect of associated bacteria on the growth of freshwater Synechococcus. [Methods] The diversity of the bacteria associated with Synechococcus was analyzed by high-throughput sequencing. The associated bacteria were isolated by plate streaking and identified based on morphological characteristics and 16S rRNA gene sequence. The impact of associated bacteria on the growth of Synechococcus FACHB-7942 was analyzed by determining the concentration of chlorophyll-a by co-culturing Synechococcus and their associated bacteria of different concentrations. Rice seed germination test was carried out to verify the growth-promoting function of the associated bacteria. [Results] The dominant genera of the associated bacteria of freshwater Synechococcus were Porphyrobacter, Rhizobium, Aquimonas, and Mesorhizobium. Two associated bacterial strains, JQ1 and JQ2, were isolated and identified as species of Rhizobium and Peribacillus, respectively. Through co-cultivation Synechococcus with different concentrations of associated bacteria and rice seed germination test, it was confirmed that JQ1 and JQ2 exerted growth-promoting effect when the ratios of bacteria to cyanobacteria were 5:1 and 15:1, respectively. JQ1 significantly improved the germination rate of rice seeds compared with JQ2, and both strains played a role in improving the seedling quality and root development. [Conclusion] The associated bacterial strains JQ1 and JQ2 at appropriate concentrations can significantly promote the growth of Synechococcus, and the application of associated bacteria in rice can improve the germination and promote the growth of rice.