The Zhelin Bay is an estuary that supports intensive aquaculture in South China. Aside from traditional nutrient inputs derived from waste water and agriculture, the increased intensification of aquaculture has accelerated eutrophication during the past decade, jeopardizing aquacultural production. Annual variations of mesozooplankton in the Zhelin Bay were described, providing baseline data for long-term ecological studies. The taxonomic composition, abundance and biomass of mesozooplankton were studied monthly from July 2001 to July 2002 at 19 stations. Collections yielded 73 taxa, including 60 species of copepods, three species of cladocerans, as well as tunicates, chaetognaths, polychaetes, medusae, ostracods, rotatori, amphipods, planktonic mollusks, pelagic larvae, and planktonic shrimps. The Zhelin Bay was dominated by small mesozooplankton, with 76% of the species smaller than 1.4 mm, and 97% of the individuals smaller than 1.0 mm. Dominant species (Paracalanus crassirostris, Oithona brevicornis,and Penilia avirostris) accounting for 60% of the total abundance were less than 0.6 mm in body length. Species diversity, biomass, and total abundance of mesozooplankton were greater in the samples collected outside the bay than inside the bay. Samples from the outer and eastern boundaries of the bay had greater biomass, diversity, and abundance than those from the inner and western boundaries. Total abundance and biomass had a unimodal annual pattern and were the greatest in August 2001 when water temperature was maximum, and the least in February 2002 when water temperature was minimum. Canonical correspondence analysis (CCA) revealed that temperature, turbidity, nutrients and salinity were the main determinants of spatial and temporal distributions of mesozooplankton in the Zhelin Bay, and six distinct zones were identified across the 19 sampling stations. The Zhelin Bay is an estuary that supports intensive aquaculture in South China. Aside from traditional nutrient inputs derived from waste water and agriculture, the increased intensification of aquaculture has accelerated eutrophication during the past decade, jeopardizing aquacultural production. Annual variations of mesozooplankton in the Zhelin The taxonomic composition, abundance and biomass of mesozooplankton were viewed monthly from July 2001 to July 2002 at 19 stations. Collections yielded 73 taxa, including 60 species of copepods, three species of cladocerans, as well as tunicates, chaetognaths, polychaetes, medusae, ostracods, rotatori, amphipods, planktonic mollusks, pelagic larvae, and planktonic shrimps. The Zhelin Bay was dominated by small mesozooplankton, with 76% of the species smaller than 1.4 mm, and 97% of the individuals smaller than 1.0 mm. Dominant species (Paracalanus crassirostris, O. ithona brevicornis, and Penilia avirostris) accounting for 60% of the total abundance were less than 0.6 mm in body length. Species diversity, biomass, and total abundance of mesozooplankton were greater in the samples collected outside the bay than inside the bay. Samples from the outer and eastern boundaries of the bay had greater biomass, diversity, and abundance than those from the inner and western boundaries. Total abundance and biomass had a unimodal annual pattern and were the greatest in August 2001 when water temperature was maximum, and the least Canonical correspondence analysis (CCA) revealed that temperature, turbidity, nutrients and salinity were the main determinants of spatial and temporal distributions of mesozooplankton in the Zhelin Bay, and six distinct zones were identified across the 19 sampling stations.