Abstract: Coral reefs contain the highest biodiversity ecosystem on Earth. In order to improve our understanding of the biodiversity and zooplankton communities, zooplankton was sampled using vertical trawls with 169 μm and 505 μm planktonic nets at 10 stations (5 within lagoon and 5 on reef flat) and one continuous observatory station from the 5^th to the 15^th of May, 2004 in the Zhubi Atoll of the Nansha Islands. A total of 96 species and 17 groups of planktonic larvae were identified, among which the greatest species number was the copepods with 65 species, followed by the planktonic larvae. The average abundance of zooplankton based on the data from 169 μm planktonic net was 926.0 ± 1,155.8 inds./m³. Decreasingly dominant groups included copepods, tunicates and larvae, while dominant species included Centropages orsinii, Acartia shuzheni, Oikopleura longicauda, O. fusifornis and Gastropoda veliger. Zooplankton community structure differed between the lagoon area and reef flat. The lagoon was characterized by high species number and abundance, a prominence of dominant species and low in species evenness indices, while the reef flat showed a more even community, likely due to relatively high levels of spatial heterogeneity in coral reefs. Diurnal variations of zooplankton were obvious that species richness and average abundance at nighttime were 4.6 and 46.2 times that of the daytime values on the reef flat, respectively. Holoplankton dominated communities both in terms of richness and were either transported from oceanic waters outside the atoll or were associated with the reef-associated itself. Both meso- and micro-zooplankton played an important role in species richness and abundance in the coral reef.