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Picophytoplankton are important primary producers in oligotrophic waters and sensitive to environmental changes. However, little is known about their ecophysiology in the northern Bering Sea with complex water masses. The distribution of picophytoplankton with their optical physiological features and physicochemical characteristics as well as water masses were investigated on the northern Bering Sea Shelf during the summer of 2008. Flow cytometry and statistical analysis including Pearson correlation analysis and cluster analysis were the main methods used. Synechococcus and picoeukaryotes were the primary existing picophytoplankton assemblages, with their respective abundances ranging from 0 to 2.69 × 10 and 0.47 × 10 to 13.20 × 10 cells l and peaking at water depths of 10-30 m with surface light levels of 30-50 %. Larger Synechococcus cells contained larger amounts of chlorophyll a (Chl a) and phycoerythrin. Low temperature, high nutrient concentrations and a high N/P value (>7) might limit cell abundance of picoeukaryotes, as shown by their close relationships. With an increase of temperature and oligotrophic freshwater input, smaller picophytoplankton would thrive and the cellular Chl a (Chl a/cell) increase with higher contribution to total Chl a. Seven water types with different physicochemical and biological characteristics were differentiated using the mini-ecosystem (a descriptor of a composite of parameters defining a composite water type community, including temperature, salinity, macronutrients and community abundance of picophytoplankton) as an indicator. They are Alaska Coastal Water, Bering Shelf Surface Water, 20-40 m of Bering Shelf Water, Bering Shelf Cold Water, Anadyr Water, Anadyr-Bering Shelf Water (Bering Sea Water) and Cold Pool. [ABSTRACT FROM AUTHOR]