We studied chlorophyll a distribution patterns and their relationship with important physico-chemical water properties based on the marine ecology investigation conducted in Southern Yellow Sea during the summer of 2006. The chlorophyll a concentration was in the range of 0.07-12.17 mg/m3 with a mean of 1.42 mg/m3. Spatial distribution of chlorophyll a generally reflected the variation gradients of salinity and nutrients, with high levels in the well mixed coastal zone and low levels in the stratified open sea region. Phytoplankton tended to be assembled near the tidal front area. Subsurface chlorophyll maximum was clearly observed and its depth was positively correlated with the transparency. Relationships between chlorophyll a concentration and the major environmental factors showed that nutrients availability was the dominant regulating factors of phytoplankton distribution at the large spatial scale, while temperature, light and zooplankton predation might also modulate the phytoplankton biomass in local regions.