The present study analyzed interannual variation of phytoplankton/Chlorophyll-a (Chl-a) distribution in the South China Sea (SCS) for the period from 1997 to 2005 using SeaWiFS-derived Chl-a data and other oceanographic data. The results show high spatial variation of Chl-a concentrations in the SCS and revealed an anomalous event in 1998. High Chl-a concentrations in the southwestern SCS in the summer season (June to August) may be related with strong Ekman Pumping and strong wind stress, whereas a jet-shape high Chl-a region offshore in western SCS was associated with coastal upwelling driven by offshore Ekman transport and Vietnamese offshore current. Chl-a concentrations in 1998 summer in the SCS were the lowest among the 7 years and were particularly low in the western SCS. At the same season, the jet-shape Chl-a region offshore of southeast Vietnam almost disappeared, and southwesterly monsoon winds and offshore current were relatively weaker in 1998. This anomalous event of low phytoplankton biomass in the SCS coincided with an El Niqo year in 1998.