Marine free-living nematode communities were studied at similar depths (~500 m) at two sides of the Antarctic Peninsula, characterised by different environmental and oceanographic conditions. At the Weddell Sea side, benthic communities are influenced by cold deep-water formation and seasonal sea-ice conditions, whereas the Drake Passage side experiences milder oceanic conditions and strong dynamics of the Antarctic Circumpolar Current. This resulted in different surface primary productivity, which contrasted with observed benthic pigment patterns and varied according to the area studied: chlorophyll a concentrations (as a proxy for primary production) were high in the Weddell Sea sediments, but low in the surface waters above; this pattern was reversed in the Drake Passage. Differences between areas were largely mirrored by the nematode communities: nematode densities peaked in Weddell stations and showed deeper vertical occurrence in the sediment, associated with deeper penetration of chlorophyll a and indicative of a strong bentho-pelagic coupling. Generic composition showed some similarities across both areas, though differences in the relative contribution of certain genera were noted, together with distinct community shifts with depth in the sediment at all locations.