The distribution of three groups of picophytoplankton were identified using flow cytometry in winter (November to December, 2013) and spring (May, 2014) in the northeastem South China Sea to understand the seasonal variation of the picophytoplankton and the effects of three water masses on them.Synechococcus was most abundant followed by Prochlorococcus, and picoeukaryotes was the minor but contributed most to the carbon biomass and Chl a.The abundances of Synechococcus and picoeukaryotes were generally higher in coastal area and continental shelf but Prochlorococcus was more abundant in continental slope and open seas.