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The investigation on community structure of standing stock of photosynthetic picoplankton: Synechococcus (Syn), Prochlorococcus (Pro) and Picoeukaryotes (Euk) and their environmental regulation mechanisms in the northern South China Sea was carried out in the summer of 1999. The results showed that the average abundances of Syn, Pro and Euk in the study sea areas were (5.0± 7.6)×104cell/cm3 (51%), (4.6±4.2)×104 cell/cm3 (47%) and (1.8±1.1)×l03 cell/cm3 (2%) respectively, and those of their carbon biomass were (12.5±18.9) μg/dm3 (74%), (2.7±2.5) μg/dm3 (16 %) and (1.7±1.0) μg/dm3 (10%). The most of high values of Syn appeared in the estuaries, coastal zone and continental shelf in the sea area to the east of Leizhou Peninsula and Hainan Island where nutrients were rich, and those appeared in the Beibu Gulfwere the second, while those appeared in continental slope and open sea were tens times lower than the above those. Its distribution in water column was mainly above the thermocline and its abundance below it sharply decreased. Two different populations of Pro were found, the surface population and deep one. The distribution pattern of the former was similar to that of Syn; while with marked difference from that of the former, the abundance and biomass of the latter markedly increased towards outer sea, continental slope and open sea where nutrients were poor; the high values in the water column mainly appeared at the bottom of euphoric zone and above the nitrocline, where it often vigorously grow. The distribution difference of Euk in the various sea areas is not as obvious as those of Syn and Pro, but it was high in coastal and shelf waters and low in continental slope and open sea. The high values in the water column were mostly appeared at the bottom of euphoric zone. This difference of distribution pattern for the three type of photosynthetic picoplankton depends on environmental effects and their ecophysiological differences.