Euphausia superba is a keystone species in Antarctic food webs. However, the continued decrease in stock density raises concerns over the resilience and adaptive potential of krill to withstand the current rate of environmental change. We undertook a transcriptome-scale approach (454 pyrosequencing) as a baseline for future studies addressing the physiological response of krill to short-term food shortage and natural UV-B stress. The final assembly resulted in a total of 26,415 contigs, 39.8% of which were putatively annotated. Exploratory analyses indicate an overall reduction in protein synthesis under food shortage while UV stress resulted in the activation of photo-protective mechanisms.