The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR, established 1982) has, in an effort to conserve Antarctic marine life, established various Southern Ocean marine protected areas (MPAs), with varying levels of protection. These include the South Orkney Islands Southern shelf MPA (2009) and Ross Sea MPA (2016) and others are now being proposed in and around East Antarctica. Mesopelagic fish (e.g. myctophids) form an important component of Southern Ocean food-webs and may contribute substantially to the biological carbon pump, which facilities the biological transfer of atmospheric carbon to the seabed. Mesopelagic fish occupy the mesopelagic zone (200-1000 m) during the daytime and most migrate vertically at night to feed at the surface. Their global biomass is between 1.6 and 16 gigatons and may yet provide a sustainable fishery of the future. To partition the Southern Ocean into distinct mesopelagic fish habitats, and therefore gain insight into the role of mesopelagic fish in Southern Ocean pelagic food-webs and ecosystem function, we must first link environmental variability with changes in mesopelagic fish biomass and behaviour.