AbstractQuantitative research on composition, biomass and production rates of zooplankton community is crucial to understand the trophic structure in coral reef pelagic ecosystems. In the present study, micro‐ (35–100 μm) and net‐ (>100 μm) metazooplankton were investigated in a fringing coral reef at Tioman Island of Malaysia. Sampling was done during the day and night in August and October 2004, and February and June 2005. The mean biomass of total metazooplankton (i.e. micro + net) was 3.42 ± 0.64 mg C·m−3, ranging from 2.32 ± 0.75 mg C·m−3 in October to 3.26 ± 1.77 mg C·m−3 in August. The net‐zooplankton biomass exhibited a nocturnal increase from daytime at 131–264% due to the addition of both pelagic and reef‐associated zooplankton into the water column. The estimated daily production rates of the total metazooplankton community were on average 1.80 ± 0.57 mg C·m−3·day−1, but this increased to 2.51 ± 1.06 mg C·m−3·day−1 if house production of larvaceans was taken into account. Of the total production rate, the secondary and tertiary production rates were 2.20 ± 1.03 and 0.30 ± 0.06 mg C·m−3·day−1, respectively. We estimated the food requirements of zooplankton in order to examine the trophic structure of the pelagic ecosystem. The secondary production may not be satisfied by phytoplankton alone in the study area and the shortfall may be supplied by other organic sources such as detritus.