To provide massive genetic resources for the Antarctic krill (Euphausia superba), we sequenced and analysed the transcriptome by using high-throughput Illumina paired-end sequencing technology. A total of 77.1 million clean reads representing ~11.0Gb data were generated. The average length of these reads was 142 bp. De novo assembly yielded 125,211 transcripts with a N50 of 690 bp. Further analysis produced 106,250 unigenes, of which 31,683 were annotated based on protein homology searches against protein databases. Gene ontology analysis showed that ion binding, organic substance, metabolic process, and cell part were the most abundantly used terms in molecular function, biological process and cellular component categories, respectively. In addition, 3067 unigenes were mapped onto 311 signal pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, 15,224 simple sequence repeats were identified from 13,535 transcripts, and 103,593 single-nucleotide polymorphisms were found from 21.6% of total transcripts. These genetic resources obtained in this study forms a good foundation for investigating gene function, and evaluating population genetic diversity for this important Southern Ocean fisheries resource, E. superba.