By using bulk and single-cell alkaline phosphatase activity (APA) assay, two cruises were carried out to study influence of mesoscale physical process (plume, upwelling) on phosphorus (P) stress of phytoplankton in northern South China Sea during summer of 2008 and winter of 2008/2009, respectively. Both bulk APA and single-cell APA results showed that P stress of phytoplankton in plume water was significantly higher than that in upwelled water, suggesting that there was serious P stress in plume area, and P stress was recovered with P input by upwelling event. APA was significantly negative with salinity in the plume area, which suggested that APA was closed coupling with DIP dissolved in the plume. Bulk APA and its size-fractionation were matched well with the model of relationship between APA and P stress. There was connection between phytoplankton dominant species and P stress, dominant species changed from Skeletonema costatum and Pseudo-nitzschia pungens to Chaetoceros and, when plume declined and P concentration went down, because species such as Skeletonema and Pseudo-nitzschia pungens were the more advantaged competitor in DIP-rich condition while Chaetoceros was the more advantaged competitor in P-poor and DOP-rich system.[Wç”?]  Our results suggest that phytoplankton suffer P-stress in most seasons, and emphasize the importance of AP in the recycling of organic P to support primary production in the P-deficient northern South China Sea.