Abstract: An extreme persistent cold anomaly was prevailing in the South China Sea in February 2008. In order to understand the effect of the cold anomaly on zooplankton community, the zooplankton composition, abundance and biomass were analyzed in the northern South China Sea in August 2007 and August 2008. A total of 467 zooplankton species representing 16 groups were identified, with 275 species in August 2007 and 351 in August 2008. Copepods were the most dominant zooplankton group in the study area. Compared with 2007, a dramatic decline was observed in the abundance of four dominant copepod species:Subeucalanus subcrassus, Temora discaudata, Nannocalanus minor and Temora turbinata in 2008. Moreover, zooplankton abundance declined from 133.37 ind./m³ in August 2007 to 75.49 ind./m³ in August 2008. In contrast, the abundance of medusa, such as Diphyes chamissonis, and tunicate, such as Doliolum denticulatum and Dolioletta gegenbauri, increased during the same season. Cluster analysis showed that there was a difference in zooplankton community structure between the two years. These variations in zooplankton communities were indicative of an anomalous oceanographic condition along with the extreme cold event in 2008.