Abstract: Zooplankton samples were collected from 24 stations in 2 investigations in the Pearl River Estuary in November 2013 (dry season) and August 2014 (wet season). The meso- and micro-zooplankton composition, abundance, distribution and community structures and the environmental influence were studied. The results showed that there were 91 and 70 zooplankton species, mainly copepods, identified in the dry and wet seasons, respectively. The number of zooplankton species increased gradually from the upper reach of the estuary to the outer waters. The abundance of zooplankton was found varying obviously with time and geographic locations. The average zooplankton abundance in the wet season (11 619.78 ind/m³) was much higher than in the dry season (1 707.13 ind/m³). Copepod was the predominant species and its abundance accounted for 80.3% and 93.0% of the total in the dry and wet seasons. They plays a key role in controlling the abundance distribution of zooplankton. Three species of copepods of Parvocalanus crassirostris, Acartiella sinensis and Acartia spinicauda were dominating in 2 investigations. The abundance of other two species, Paracalanus parvus and Bestiolina amoyensis varied distinctly with seasons. Hierarchical cluster analysis classified 3 zooplankton groups from 2 seasons. Correlation analysis indicated that the dynamics of zooplankton community was determined by several factors in which the salinity was the most important abiotic factor.