In this study, species composition, species abundance, and seasonal variation of phytoplankton were surveyed in six Fujian bays, including Ningde, Putian, Meizhou, Xiamen, Zhangpu, and Dongshan from 2010 to 2011. During these surveys, 206 species belonging to 102 genera were identified, and diatoms were the dominant species followed by dinoflagellate species. The bay with the most species was Putian (110), followed by Dongshan (106), Xiamen (100), Zhangpu (95), Meizhou (86), and the least number of species was found in Ningde. Using a seasonal analysis, the amount of phytoplankton species in northern bays was higher than that in the southern bays in the spring, and the reverse was true in the fall. Interestingly, the abundance of phytoplankton species was higher in northern bays than in southern bays in the spring and the reverse was found in the fall. The diversity index ranged from 1.15 to 3.05 in the spring, and was highest in Dongshan, and lowest in Ningde. In the fall, the highest diversity index value was found in Dongshan, and the lowest was found in Xiamen. The results indicated that phytoplankton diversity in this area was mainly controlled by the growth and decline of the Fujian-Zhejiang coastal current and the South China Sea warm current. Compared with historical data, the abundance of phytoplankton has increased, and the species which adapt to high nutrient concentrations become main dominant species.