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The aim of this study was to elucidate how flooding of the Changjiang River affects the assemblage composition of phycoerythrin-rich (PE-rich) Synechococcus at the surface of the East China Sea (ECS). During non-flooding summers (e.g., 2009), PE-rich Synechococcus usually thrive at the outer edge of the Changjiang River diluted water coverage (CDW; salinity ≤31 PSU). In the summer of 2010, a severe flood occurred in the Changjiang River basin. The plentiful freshwater injection resulted in the expansion of the CDW over half of the ECS and caused PE-rich cells to show a uniform distribution pattern, with decreased abundance compared with the non-flooding summer. The phylogenetic diversity of 16S rRNA gene sequences indicated that the flooding event also shifted the picoplankton community composition from being dominated by Synechococcus, mainly attributed to the clade II lineage, to various orders of heterotrophic bacteria, including Actinobacteria, Flavobacteria, α- Proteobacteria, and γ- Proteobacteria. As an increasing number of studies have proposed that global warming might result in more frequent floods, combining this perspective with the information obtained from our previous [] and this studies yield a more comprehensive understanding of the relationship between the composition of the marine Synechococcus assemblage and global environmental changes. [ABSTRACT FROM AUTHOR]