Seasonal variations in zooplankton abundance, biomass, species diversity and community structure were investigated in the Sanmen Bay, China. Samples were collected from 15 stations, on the seasonal basis, in April (spring), July (summer) and October 2005 (autumn) and January 2006 (winter), respectively. The results show that zooplankton species number, abundance and biomass varied widely and had distinct spatial heterogeneity in the Sanmen Bay. A total of 72 species of zooplankton belonging to 56 genera and 17 groups of pelagic larvae were identified. The zooplankton species richness was strongly related to salinity. Based on hierarchical cluster analysis, zooplankton in this study area were classified into three groups: coastal, neritic and pelagic groups, which corresponded to the upper, middle and lower portion of the Sanmen Bay, respectively. The coastal low-saline species were dominant in the study area. The zooplankton abundance and biomass reached a peak in summer, moderate in spring and autumn, and the lowest in winter. Zooplankton abundance decreased from the upper to lower portion of the bay in April, when the highest biomass occurred in the middle portion of the bay. There were the same spatial distribution patterns for the biomass and abundance in July, with the maximum in the middle of the bay. However, zooplankton abundance was the highest in the middle of the bay in October, when maximum biomass occurred near the lower of the bay. Zooplankton abundance and biomass were evenly distributed in the Sanmen Bay in January. Spatial and temporal variations in zooplankton and their relationship with environmental factors were also analyzed. The BIOENV results indicate that the combination of chlorophyll a (Chl-a), salinity, dissolved inorganic nitrogen (DIN), dissolved oxygen (DO) and silicate (SiO3) was responsible for the variations in zooplankton community structure in the Sanmen Bay. The environmental changes played an important role in changes in the zooplankton community structure in the Sanmen Bay.