The gradient in the partial pressure of carbon dioxide (pCO2) across the air-sea boundary layer is the main driving force for the air-sea CO2 flux. Global data bases for surface seawater pCO2 are actually based on pCO2 measurements from several meters below the sea surface, assuming a homogeneous distribution between the diffusive boundary layer and the upper top meters of the ocean. Compiling vertical profiles of pCO2, temperature, and dissolved oxygen in the upper 5–8 m of the ocean from different biogeographical areas, we detected a mean difference between the boundary layer and 5 m pCO2 of 13 ± 1 µatm. Temperature gradients accounted for only 11% of this pCO2 gradient in the top meters of the ocean; thus, pointing to a heterogeneous biological activity underneath the air-sea boundary layer as the main factor controlling the top meters pCO2 variability. Observations of pCO2 just beneath the air-sea boundary layer should be further investigated in order to estimate possible biases in calculating global air-sea CO2 fluxes.