Climate change-related alterations of Antarctic sea-ice habitats will significantly impact the interaction of ice-associated organisms with the environment, with repercussions on ecosystem functioning. The nature of this interaction is poorly understood, particularly during the critical period of winter–spring transition. To investigate the role of sea-ice and underlying water-column properties in structuring under-ice communities during late winter/early spring, we used a Surface and Under Ice Trawl to sample animals and environmental properties in the upper 2-m layer under the sea ice in the northern Weddell Sea from August to October 2013. The area of investigation was largely homogeneous in terms of hydrography and sea-ice coverage. We hypothesised that this apparent homogeneity in the physical regime was mirrored in the structure of the under-ice community. The under-ice community was numerically dominated by the copepods Stephos longipes, Ctenocalanus spp. and Calanus propinquus (altogether 67 %), and furcilia larvae of Antarctic krill Euphausia superba (30 %). In spite of the apparent homogeneity of the environment, abundance and biomass distributions at our sampling stations indicated the presence of three community types, following a geographical gradient in the investigation area: (1) high biomass, krill-dominated in the west, (2) high abundance, copepod-dominated in the east, and (3) low abundance, low biomass at the ice edge. Combined analysis with environmental data indicated that under-ice community structure was correlated with sea-ice coverage, chlorophyll a concentration, and bottom depth. The heterogeneity of the Antarctic under-ice community was probably also driven by other factors, such as advection, sea-ice drift, and seasonal progression. The response of under-ice communities to changing sea-ice habitats may thus considerably vary seasonally and regionally.