Zooplankton samples were collected from three oceanographic cruises during February-March, 1999 (dry periods), August 1999 (flood periods) and February-March 2000 (dry periods), respectively, to investigate the abundance and distribution of zooplankton in Yangtze River estuary due to season variations and other main factors. The results showed that the average abundance of zooplankton was as low as 79.07 ind/m3 during the dry periods in 1999. Two high abundance areas were found inside and outside of the estuary with a gradient of gradually decrease from the estuary to the ocean. The distribution of dominant species during that time period was determined. In contrast, the average abundance of zooplankton during the flood periods in 1999 was as high as 300.89 ind/m3 and gradually increased from estuary towards open ocean. A patch distribution pattern was observed. A similar dry periods distribution pattern was repeated during the dry periods in 2000. Copepoda accounted for 95.54%, 85.82% and 84.83%of total zooplankton during the February-March, 1999, August 1999 and Febuary-March 2000 samplings, respectively. In this study, we found that, Copepoda was the predominant species and played a key role in controlling the abundance and distribution of zooplankton and distribution of dominant species was considerably influenced by the tidal stage. The regression analysis showed no linear correlation between zooplankton abundance and salinity during the dry periods. However, there exists significant linear correlation during the flood periods (r=0.9341, n=8）. In addition, the seasonal variation of zooplankton abundance is closely associated with temperature, river discharge, ocean currents and food.