Dissolved inorganic phosphorus (DIP) concentrations in the oligotrophic surface waters of the South China Sea decrease from ∼20 nM in March 2000 to ∼5 nM in July 2000, in response to seasonal water column stratification. These minimum DIP concentrations are one order of magnitude higher than those in the P-limited, iron-replete stratified surface waters of the western North Atlantic, suggesting that the ecosystem in the South China Sea may be limited by bioavailable nitrogen or some trace nutrient rather than DIP. Nutrient enrichment experiments using either nitrate, phosphate or both indicate that nitrogen limits the net growth of phytoplankton in the South China Sea, at least during March and July 2000. The fixed nitrogen limitation may result from the excess phosphate (N:P<16) transported into the South China Sea from the North Pacific relative to microbial population needs, or from iron control of nitrogen fixation. The iron-limited nitrogen fixation hypothesis is supported by the observation of low population densities of Trichodesmium spp. (<48 × 103 trichomes/m3), the putative N2 fixing cyanobacterium, and with low concentrations of dissolved iron (∼0.2–0.3 nM) in the South China Sea surface water. Our results suggest that nitrogen fixation can be limited by available iron even in regions with a high rate of atmospheric dust deposition such as in the South China Sea.