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Environmental changes driven by intense human disturbance and natural processes govern the abundance and distribution characteristics of two picophytoplankton groups (Synechococcus and picoeukaryotes). Picophytoplancton and high DNA (HDNA) and low DNA (LDNA) bacterial groups, identified by flow cytometry, were assessed during the autumn monsoon transition period in Daya Bay (South China Sea). The abundance of Synechococcus and picoeukaryotes ranged from 2.16 × 104 to 1.45 × 105 cell mL–1 and from 0.78 × 103 to 7.95 × 103 cell mL–1, respectively. The abundance of HDNA bacteria in surface water (mean: 5.58 × 105 cell mL–1) was greater than in bottom water (mean: 3.74 × 105 cell mL–1), with significant difference (n = 12, P = 0.05). The difference in LDNA abundances between surface (mean: 7.06 × 105 cell mL–1) and bottom (mean: 4.83 × 105 cell mL–1) waters was insignificant (n = 12, P > 0.05). The results of the principal component analysis showed that both picophytoplankton (Synechococcus and picoeukaryotes) and bacteria (HDNA and LDNA) were positively related to nutrients (NO3-N, NH4-N, and SiO3-Si). Three subsystems in the bay were identified as follows: the west and east parts, the central and northwest parts, and the mouth and central part.