Despite the distance of Antarctica and the Southern Ocean to primary source regions of organochlorine pesticides, such as hexachlorobenzene (HCB) and hexachlorocyclohexanes (HCHs), these organic pollutants are found in this remote region due to long range atmospheric transport and deposition. This study reports the gas- and aerosol-phase concentrations of α-HCH, γ-HCH, and HCB in the atmosphere from the Weddell, South Scotia and Bellingshausen Seas. The atmospheric samples were obtained in two sampling cruises in 2008 and 2009, and in a third sampling campaign at Livingston Island (2009) in order to quantify the potential secondary sources of HCHs and HCB due to volatilization from Antarctic soils and snow. The gas phase concentrations of HCHs and HCB are low, and in the order of very few pg m−3 α-HCH and γ-HCH concentrations were higher when the air mass back trajectory was coming from the Antarctic continent, consistent with net volatilization fluxes of γ-HCH measured at Livingston Island being a significant secondary source to the regional atmosphere. In addition, the Southern ocean is an important net sink of HCHs, and to minor extent of HCB, due to high diffusive air-to-water fluxes. These net absorption fluxes for HCHs are presumably due to the role of bacterial degradation, depleting the water column concentrations of HCHs in surface waters and driving an air–water disequilibrium. This is the first field study that has investigated the coupling between the atmospheric occurrence of HCHs and HCB, the simultaneous air–water exchange, soil/snow-air exchange, and long range transport of organic pollutants in Antarctica and the Southern Ocean. •Concentrations of HCHs and HCB are low (few pg m−3) in the Southern Ocean surrounding the Antarctic Peninsula.•Antarctic snow is a secondary source of HCHs and HCB to the regional atmosphere.•The biological and degradative pumps have an influence on the atmospheric deposition of HCH and HCBs to the Southern Ocean.