Responses of Prochlorococcus (Pro), Synechococcus (Syn), pico-eukaryotes (Euk) and heterotrophic bacteria (Bact) in pelagic marine ecosystems to external nutrient perturbations were examined using nitrogen- (N), phosphorus- (P), iron- (Fe), and cobalt- (Co) enriched incubations in the South China Sea in November 1997. Variations in abundance of the 4 groups of microorganism and cellular pigment content of the autotrophs during incubation were followed by flow-cytometric measurements for seven days. During the incubation, Syn and Euk showed a relatively higher demand on Fe and N, while Pro required higher levels of Co and P. The Fe was inadequate for all the organisms in the deep euphotic zone (75 m) of the study area. The experimental results also implied that biological interaction among the organisms played a role in the community structure shift during the incubation. It seemed that besides the effects of temperature, there are some other physical and chemical limitations as well as impacts from biological interactions on Pro distribution in coast waters.