Background The Antarctic krill Euphasia superba is a keystone species in the Antarctic food chain. Not only is it a significant grazer of phytoplankton, but it is also a major food item for charismatic megafauna such as whales and seals and an important Southern Ocean fisheries crop. Ecological data suggest that this species is being affected by climate change and this will have considerable consequences for the balance of the Southern Ocean ecosystem. To gain a comprehensive understanding of how this organism functions and its interactions with the environment, detailed physiological and molecular studies are critical. These will provide fundamental data for life history studies, energy budget calculations and food web models. There is currently a paucity of molecular data for this species and this investigation seeks to redress this issue. Results A 454 transcriptome of E. superba was generated resulting in 22,177 contigs with an average size of 492bp (ranging between 137 and 8515bp). Blast sequence similarity searching assigned putative function to 25% of these contigs. In depth analysis of the data revealed an extensive catalogue of the cellular chaperone systems and the major antioxidant proteins. Full length sequences were characterised for the chaperones HSP70, HSP90 and antioxidant the super-oxide dismutases, with the discovery of potentially novel duplications of these genes. The sequence data contained 41,470 microsatellites and 17,776 Single Nucleotide Polymorphisms(SNPs/INDELS), providing a resource for population and also gene function studies. Conclusions Is the stenothermal nature of Antarctic marine species solely a result of adaptation to living in a cold constant environment for so long, or is it a trade-off effect of survival? This paper details the first 454 generated data for a pelagic Antarctic species or any pelagic crustacean globally. Highly expressed genes included classical "stress proteins" such as the heat shock proteins and we discuss these findings with relevance to understanding the cost of living in the cold and the requirement for trade-offs in cellular energetics. This data will provide a major resource for future physiological work on krill, but in particular a suite of "stress" genes for studies understanding marine ectotherms capacities to cope with environmental change.