Antarctic Krill (Euphausia superba) is a ‘keystone species’ in the Southern Ocean providing the main source of food for many taxa high in the food chain such as baleen whales, penguins and seals. Despite its ecological and economic importance, research into krill and other crustacean diseases remains a deficit area with little to nothing known about infection dynamics. Over the past century the waters of Antarctic krill northern distribution limit have experienced significant warming. In a changing environment, disease agents that require specific temperatures for growth may be able to survive and infect across an altered geographic range. In this paper we present the initial findings from a histological survey of krill from the Southern Ocean. In the present study and for the first time, krill were sampled for a gregarine parasite along a south-north gradient over several water masses, moving from the ice edge to the open ocean onto the shelf in 48.3. The presented paper offers for the first time a systematic histological analysis of normal, healthy organs of krill, creating a histological atlas which can provide a baseline for future pathogen research, as well as an atlas of infected tissue. This paper further shows circumstantial evidence for a viral infection in around 1% of sampled krill. The known gregarine krill parasite Cephaloidophora pacifica has previously not been shown to occur as far north as in the presented report. Studies on the diseases of wild crustaceans are severely lacking, despite their importance as components of the global food chain, and krill are no exception to this with very few studies carried out on their pathogen fauna. Only when this information is gathered can we accurately model future changes and therefore predict impact on the other species that rely on crustaceans as key components of marine food chains.