Based on continuous measuring of pCO2 and other carbon parameters in the shellfish beds, shellfish-algae co-culture areas and algae farming areas of Sanggou Bay from 27th to 29th May, 2012, as well daily observation in the shellfish beds, the distribution characteristics and affecting factors of pCO2 between air-sea interface in the different aquaculture zones of Sanggou Bay were discussed in this paper. It was found that Chl-a was extremely high during the investigations. As a result, dissolved oxygen was always saturated, even up to 140% saturation, while a large amount of inorganic carbon was strongly consumed by photosynthesis. Thus, this area was considered to be a CO2 sink.More specifically, pCO2 of the shellfish beds was small compared to that of the shellfish-algae co-culture area, algae farming area and coastal zones. Undoubtedly, this investigation is not enough to prove that Sanggou Bay is a CO2 sink, but more observations are still needed in large temporal-spatial scales in order to answer the questions such as how much the resuspension and degradation of the deposited particulate organic matter contributes to the pCO2 in the water-air interface, and how much the particulate organic matter is actually buried, etc.