Recent, rapid climate change is now well documented in the Antarctic, particularly in the Antarctic Peninsula region. One of the most evident signs of climate change has been ice shelf collapse; overall, 87% of the Peninsula’s glaciers have retreated in recent decades. Ice shelf collapse will lead to the loss of existing marine habitats and the creation of new habitats. In general, fauna under ice shelves exist in oligotrophic conditions, and because ice shelf collapse may lead to greater nutrient input, there may be consequent loss of some species or communities. Colonisation of new habitats after ice shelf collapse may simply include species from areas that are immediately adjacent to the collapsed ice shelf; however, other complex processes may also take place as warmer waters may create opportunities for species to return that were last present during the last interglacial, a warmer period than at present. In addition, altered ecosystem dynamics may allow new species to invade as ocean warming potentially removes physiological barriers that have previously led to the isolation of the Antarctic fauna. Habitats revealed by collapsed ice shelves offer unique scientific opportunities. Given the complexity of the possible interactions and the need to study these in the absence of any other human induced perturbation, we recommend that commercial fishing activities should not be permitted in these habitats. We suggest that in Subareas 48.1, 48.5 and 88.3, areas under existing ice shelves should be preserved for scientific study as Marine Protected Areas (MPAs). We recommend that the boundaries of these areas should henceforth remain fixed, even if the ice shelves recede or collapse in the future. Designation of areas under ice shelves as MPAs for scientific study would fulfil one of the recommendations made by the Antarctic Treaty Meeting of Experts in 2010.