Xinghuawan Bay is the biggest bay in northern Fujian Province of China. A comprehensive investigation on the population of zooplankton was conducted at 9 stations seasonally in 2006. Total 124 zooplankton species with 10 larvae were identified during the investigation. Among which 42, 89, 71, and 20 species occurred in spring, summer, autumn, and winter, respectively. All these zooplankton could be divided into three ecotypes, including offshore warm-water group, offshore warm-temperature group and eurytopic group. There were 15 dominant species during sampling period. Among which jellyfish dominated the community in spring, summer and autumn, copepods dominated in spring, autumn and winter, chaetognatha dominated in autumn. Seasonal variations of horizontal distribution of biomass and abundance of zooplankton were significantly correlated with both water temperature and salinity. Community cluster analysis indicated the similarity of the summer and autumn groups of zooplankton, and mouth area group and inner bay group could be divided in all seasons. Although the zooplankton communities in this study had not represented significant difference compared to the pattern in the 1980s, the health of marine ecosystem of Xinghuawan Bay is threatened by increasing economic activities (e.g. power plants) now and should pay more concern.