Our study deals with the lipid biochemistry of the krill community in the ecosystem of the high Arctic Kongsfjord (Svalbard). During the last decades, Kongsfjord experienced a change in krill species composition due to recent increased advection of Atlantic water masses carrying characteristic boreal as well as subtropical-boreal euphausiids into the ecosystem. The lipid biochemistry and trophic relationships of the species recently inhabiting the Arctic water masses are scarcely known, although a change in a krill population may have a significant impact on the ecosystem. A comparison of nutrition and energy storage strategies, stable isotopes, lipid profiles and fatty acid compositions showed remarkable differences between the krill species. These reflected the diverse feeding behaviours and specific adaptations to the environments of their origin: the boreal Meganyctiphanes norvegica and subtropical Nematoscelis megalops appear more carnivorous, have significantly lower mean lipid contents (29 % and 10 %, respectively) and a different energy storage pattern (triacylglycerols and polar lipids, respectively) than the arcto-boreal Thysanoessa inermis, which consists of up to 54 % of lipids mainly stored as wax esters (> 40 %). These differences may have significant implications for the rapidly changing marine food-web of Kongsfjord - especially for higher trophic levels relying on the nutritional input of animal lipids.