Hexachlorocyclohexanes (HCHs) are ubiquitous organic pollutants derived from pesticide application. They are subject to long-range transport, persistent in the environment, and capable of accumulation in biota. Shipboard measurements of HCH isomers (α-, γ- and β-HCH) in surface seawater and boundary layer atmospheric samples were conducted in the Atlantic and the Southern Ocean in October to December of 2008. ΣHCHs concentrations (the sum of α-, γ- and β-HCH) in the lower atmosphere ranged from 12 to 37 pg m−3 (mean: 27 ± 11 pg m−3) in the Northern Hemisphere (NH), and from 1.5 to 4.0 pg m−3 (mean: 2.8 ± 1.1 pg m−3) in the Southern Hemisphere (SH), respectively. Water concentrations were: α-HCH 0.33–47 pg l−1, γ-HCH 0.02–33 pg l−1 and β-HCH 0.11–9.5 pg l−1. Dissolved HCH concentrations decreased from the North Atlantic to the Southern Ocean, indicating historical use of HCHs in the NH. Spatial distribution showed increasing concentrations from the equator towards North and South latitudes illustrating the concept of cold trapping in high latitudes and less interhemispheric mixing process. In comparison to concentrations measured in 1987–1999/2000, gaseous HCHs were slightly lower, while dissolved HCHs decreased by factor of 2–3 orders of magnitude. Air-water exchange gradients suggested net deposition for α-HCH (mean: 3800 pg m−2 day−1) and γ-HCH (mean: 2000 pg m−2 day−1), whereas β-HCH varied between equilibrium (volatilization: 〈0–12 pg m−2 day−1) and net deposition (range: 6–690 pg m−2 day−1). Climate change may significantly accelerate the release of "old" HCHs from continental storage (e.g. soil, vegetation and high mountains) and drive long-range transport from sources to deposition in the open oceans. Biological productivities may interfere with the air-water exchange process as well. Consequently, further investigation is necessary to elucidate the long term trends and the biogeochemical turnover of HCHs in the oceanic environment.