Understanding the relationship between the zooplankton distribution and salinity may provide key information to under-stand ecosystem function under the condition of a global mean sea level rise caused by global climate change. However, little is known about how increasing salinity level will affect the entire zooplankton community on a large scale. Here we completed 1 year of field investigations on the Pearl River Estuary and analyzed the distribution and structure of the zooplankton community. A total of 68 zooplankton species were identified during the survey. The number and diversity (richness, evenness, Shannon index, and Simp- son's index) of the zooplankton species decreased as salinity increased from 0.10 to 21.26. Salinity negatively affected the abun- dances of rotifers, cladocerans, and total zooplankton, while it had little effect on copepod abundance. Some salt-tolerant species, such asKeratella tropica,Polyarthra vulgaris, andParacalanus crassirostris,survived at high-salinity sites. A pattern was observed at all sites: the peak in copepod abundance always occurred when rotifers were abundant (sites S1 and S2) or after rotifer abundance reached a maximum level (sites S3, S4, and S5). In general, salinity was the most important environmental factor shaping zooplank-ton biodiversity and abundance. This study provides insight into potential biodiversity and structure of the zooplankton community in response to salinity change.