Phytoplankton community was investigated in the cage culture area of Daya Bay during a diurnal cycle. Two rainfalls occurred during the course of the experiment and decreased the surface seawater salinity in the aquaculture area. A total of 38 species were identified, of which the dominant species included Pseudo-nitzschia spp. and Skeletonema costatum. Water stratification obstructed the vertical migration of dinoflagellates. Statistical analysis indicated that Synechococcus showed negative relationship with silicate and ammonia, which indicated that Synechococcus adapted to grow at oligotrophic environment. Phytoplankton community structure implied the risk of Pseudo-nitzschia spp. blooms in the aquaculture area of Daya Bay.
