The Southern Ocean supports diverse and unique ecosystems that have been impacted by more than twocenturies of exploitation and are now experiencing rapid changes in ocean temperature and seasonal icecover due to climate warming. Understanding and projecting responses of Southern Ocean marine ecosystemsto changing climate conditions and direct human impacts, such as fisheries, requires integratedecosystem analyses at scales previously unexplored. Here we consider the main ecological and modellingchallenges in predicting the responses of Southern Ocean ecosystems to change, and propose three interlinkedfocus areas that will advance the development of integrated models for Southern Ocean ecosystems.The first focus area is development of fundamental understanding of the factors that determinethe structure and function of the food webs at multiple scales. Ecological research in the Southern Oceanis often centred on key species or localised systems, a tendency which is reflected in existing food weband ecosystem models. To build on this, a systematic analysis of regional food web structure and functionis required. The second focus area is development of a range of mechanistic models that vary in their resolutionof ecological processes, and consider links across physical scales, biogeochemical cycles and feedbacks,and the central role of zooplankton. These two focus areas underlie the third, which isdevelopment of methodologies for scenario testing across a range of trophic levels of the effects of pastand future changes, which will facilitate consideration of the underlying complexity of interactions andthe associated uncertainty. The complex nature of interactions determining Southern Ocean ecosystemstructure and function will require new approaches, which we propose should be developed within ascale-based framework that emphasises both physical and ecological aspects.