Regional climate change is now known to be well established 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 new marine habitats and to biological colonisation. Colonisation of these habitats 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 also allow new alien species to invade as ocean warming potentially removes physiological barriers that have previously led to the isolation of the Antarctic benthos. 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 locations under existing ice shelves (as at 2010) should be created as no take Marine Protected Areas, and that the boundaries of these areas should henceforth remain fixed, even if the ice shelves recede or collapse in the future.