The South China Sea (SCS) is surrounded by developing countries in Southeast Asia, where persistent organic pollutants (POPs), such as organochlorine pesticides (OCPs), are still used legally or illegally, and are of concern. Yet little is known about the distribution of OCPs in the water and atmosphere over SCS, as well as their air-sea equilibrium status and time trends. In this study, ship-board air samples and surface seawater collected in the northern SCS between September 6 and 22, 2005 were analyzed for selected OCPs. The measured OCP concentrations in the atmosphere over the northern SCS were influenced by proximity to source regions and air mass origins. The highest atmospheric OCP concentrations were found at sampling sites adjacent to continental South China. OCPs in surface seawater showed significant spatial variations, with the highest concentration observed in a water sample from off Vietnam. The coastal currents were suggested to play a key role in the delivery of waterborne OCPs in the northern SCS. Time trend, land outflow, and air-sea exchange of selected OCPs in the SCS were investigated, by comparison of this dataset with historical data.