The Antarctic krill (Euphausia superba) provides central ecosystems services to the Southern Ocean grazing on (phyto/zoo)plankton and constituting the dominant food source for higher trophic levels. Krill was caught during the RVIB Nathanie B. Palmer Cruise NBP1606 (AMLR2016) at 3 different stations alongside the Bransfield Strait of the Antarctic Peninsula. To generate a transcriptomic assembly, RNA samples was extracted from 4 dofferent compartments of female animals and sequenced using both long- and short-reads sequencing technology. The transcriptome-proteome compendium of krill established in the present study provides a valuable basis for future studies on krill biology (e.g., metabolism, development, migration behaviour), for krill's contribution to organic matter turnover in the Southern Ocean, as well as for multilevel biotechnological prospecting.