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Marine picophytoplankton (Pico) as a major contributor to primary productivity in oligotrophic waters, play a very important role in marine material cycle and energy conversion, and their key role in the carbon cycle and global climate change is increasingly emphasized. To study the factors affecting the dynamic distribution of Synechococcus, Prochlorococcus, and picoeukaryotes in the East China Sea (ECS), a marginal sea of the Northwest Pacific, we investigated 27 stations in May 2017, and collected 148 samples of Pico and nutrients from the surface to the bottom. By means of flow cytometry, the abundance of Pico was measured, and then we estimated the carbon biomass and analyzed the distribution of Pico. Finally, combined with the ECS unique geographical situation and hydrological regime, we evaluated various factors affecting the Pico in the ECS. In Pico community, the picoeukaryotes cell abundance was between 0.49×102−1.44×104 cells/mL. Prochlorococcus ranged from 1.36×103−3.47×104 cells/mL and Synechococcus ranged from 0.69×103−1.15×105 cells/mL. Synechococcus was the most, both in abundance and in carbon biomass. Picoeukaryotes were the least in abundance, but has larger contribution to carbon biomass than Prochlorococcus. Water temperature, salinity, and stability of water column influenced Pico distribution. Picoeukaryotes were abundant in the shelf sea, whereas Synechococcus and Prochlorococcus were detected in the northeast of Taiwan, China. This study provided basic information for the study of Pico communities in the ECS and its adjacent marine ecosystem. [ABSTRACT FROM AUTHOR]