Abstract: According to the four seasonal cruises on the zooplankton in the northern waters of Nanao Islands in April, August, November 2011 and February 2012, the species compositions, ecological groups, abundance, biomass, dominant species and diversity index of the zooplankton were investigated and the correction between water masses and zooplankton was evaluated. A total of 158 zooplankton species were identified, including 46 species in spring, 104 species in summer, 96 species in autumn and 44 species in winter. The zooplankton community structure varied with the seasons, including three main ecological groups, such as warmwater neritic species, warmwater oceanic species and warmwater euryhaline species. The abundance of the zooplankton was 292.31 indm- 3 in summer, 143.25 indm-3 in winter, 116.65 indm-3 in autumn and 26.48 indm-3 in spring. The zooplankton biomass was 140.15 mgm-3 in summer, 126.75 mgm-3 in autumn, 89. 84 mgm-3 in winter and 37.96 mgm-3 in spring. Most of the dominant species were neritic species and Centropages tenuiremis was only one of the annual dominant species. The species diversity of zooplankton was the highest in summer and the lowest in winter. The zooplanktonic ecological characteristics which were closely related with the seasonal variation of water masses, especially the runoffs, had the typical subtropical estuary ecological characteristics in the zone.