Environmental characteristics and phytoplankton community structure were investigated in two aquaculture areas in Dapeng Cove of Daya Bay, South China Sea, between April 2005 and June 2006. Phytoplankton abundance ranged between 5.0 and 8877.5 cells/mL, with an average of 751.8 cells/mL. The seasonal cycle of phytoplankton were demonstrated by frequent oscillations, with recurrent high abundances from late spring to autumn and a peak stage in late winter. Diatoms were the predominant phytoplankton group, accounting for 93.21% of the total abundance. The next most abundant group was the dinoflagellates, which made up only 1.24% of total abundance. High concentrations of Alexandrium tamarense （Lebour） Balech with a maximum of 603.0 cells/mL were firstly recorded in this area known for high rates of paralytic shellfish poisoning （PSP） contamination. Temperatures and salinities were within the suitable values for the growth of phytoplankton, and were important in phytoplankton seasonal fluctuations. The operation of the Daya Bay Nuclear Power Station （DNPS） exerts influences on the phytoplankton community and resulted in the high abundances of toxic dinoflagellate species during the winter months. Dissolved inorganic nitrogen （DIN） and dissolved silicate （DSi） were sufficient, and rarely limited for the growth of phytoplankton. Dissolved inorganic phosphorus （DIP） was the most necessary element for phytoplankton growth. The enriched environments accelerated the growth of small diatoms, and made for the shift in predominant species from large diatom Rhizosolenia spp. to chain-forming diatoms such as Skeletonema costatum, Pseudo-nitzschia spp. and Thalassiosira subtilis.
