The zooplankton species compositions and dominant species in the Daya Bay were studied based on 124 samples collected from seasonal surveys conducted in December 2007 and March, May, and September 2008. A total number of 284 zooplankton species were recorded in the surveys. We found large seasonal changes in zooplankton compositions with an average ratio of 62.3% of species seasonal subrogation. We also found that there were apparent dominant species and the dominant species changed greatly between seasons. Noctiluca miliaris was the first dominant species in winter and spring and Dolioletta gegenbauri and Sagitta enflata dominated in the other two seasons, while the other 13 species were seasonal dominant species only found in a single season. The clear seasonal succession of zooplankton compositions and dominant species was a reflection of the increased amplitude of seasonal variations in environmental conditions in the Daya Bay. Compared with past records, the seasonal subrogation ratio of zooplankton species has been increased, the dominant species changed from Copepoda to Protista, and their dominance became higher. This indicates that the stability of zooplankton community has been reduced. The increased water temperature in the Daya Bay has changed the life cycle of the warm-water zooplanktons. The peak season of zooplankton abundances shifts from August to May or October when water temperature is lower, the warm-water zooplankton species occur in all seasons, and the amplitudes of seasonal variations in their abundances have been reduced. Because of the increased nutrient levels in the Daya Bay, the dominance of the red-tide species of Noctiluca miliaris has been greatly increased, especially in winter and spring when the water temperature is lower, and the highest abundances are found in the waters affected warm water discharges from the Daya Bay Nuclear Power Plant.