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Based upon 14 field surveys conducted between 2003 and 2008, we showed that the seasonal pattern of sea surface partial pressure of CO₂ (<i>p</i>CO₂) and sea–air CO₂ fluxes differed among four different physical–biogeochemical domains in the South China Sea (SCS) proper. The four domains were located between 7 and 23° N and 110 and 121° E, covering a surface area of 1344 × 10³ km² and accounting for ~ 54% of the SCS proper. In the area off the Pearl River estuary, relatively low <i>p</i>CO₂ values of 320 to 390 μatm were observed in all four seasons and both the biological productivity and CO₂ uptake were enhanced in summer in the Pearl River plume waters. In the northern SCS slope/basin area, a typical seasonal cycle of relatively high <i>p</i>CO₂ in the warm seasons and relatively low <i>p</i>CO₂ in the cold seasons was revealed. In the central/southern SCS area, moderately high sea surface <i>p</i>CO₂ values of 360 to 425 μatm were observed throughout the year. In the area west of the Luzon Strait, a major exchange pathway between the SCS and the Pacific Ocean, <i>p</i>CO₂ was particularly dynamic in winter, when northeast monsoon induced upwelling events and strong outgassing of CO₂. These episodic events might have dominated the annual sea–air CO₂ flux in this particular area. The estimate of annual sea–air CO₂ fluxes showed that most areas of the SCS proper served as weak to moderate sources of the atmospheric CO₂, with sea–air CO₂ flux values of 0.46 ± 0.43 mol m⁻² yr⁻¹ in the northern SCS slope/basin, 1.37 ± 0.55 mol m⁻² yr⁻¹ in the central/southern SCS, and 1.21 ± 1.48 mol m⁻² yr⁻¹ in the area west of the Luzon Strait. However, the annual sea–air CO₂ exchange was nearly in equilibrium (−0.44 ± 0.65 mol m⁻² yr⁻¹) in the area off the Pearl River estuary. Overall the four domains contributed (18 ± 10) × 10¹² g C yr⁻¹ to the atmospheric CO₂.