Zooplankton samples were collected from seven oceanographic censuses in the southern Yellow Sea in June in 1959 and 20002009. The interannual changes in abundance of different zooplankton functional groups were studied with simultaneously measured temperature-salinity data and long-term change data of seawater temperature. The results show that both giant crustaceans and chaetognaths had high abundance and fluctuated remarkably; both the abundance was similar between 1959 and 20002009, of which the lowest abundance occurred in 2003 and 2000, respectively. The abundance of large copepods, dominated by Calanus sinicus, was significantly higher in 20002009 than that in 1959, and the fluctuation ranges were 203524500 and 9121330 ind/m~2 in the two periods, respectively. Small jellyfish and salps usually presented low abundance, but both increased dramatically in 2007 for being 4.8-fold and 88.5-fold, respectively, of the highest mean abundance in other years. Giant crustaceans and chaetognaths varied widely in the Yellow Sea Cold Water Mass region and tidal front region, respectively, while small jellyfish and salps fluctuated widely in the western shallow region. We believe that the increased copepod abundance was resulted from increased nutrition and over-fishing, while the dramatic fluctuation of gelatinous zooplankton was due to environmental variation under global climate change.