Hyas araneus is a widely distributed crustacean species, which has increasingly become an important organism for pysiological studies investigating the response to environmental changes. Unfortunately, the low availability of genomic data for crustaceans results in a limitation of genomic research investigating the genetic basis of these responses. Within the framework of this study,we generated a transcriptome using the 454 GS FLX sequencing technology in combination with an Illumina HiSeq sequencing approach. On this basis, we used global gene expression profiling through RNA-Sequencing to study the transcriptional responses to ocean acidification and warming in gills of the boreal spider crab Hyas araneus exposed medium-term (10 weeks) to intermediate (1,120 µatm) and high (1,960 µatm) PCO2 at different temperatures (5°C and 10°C). Our study provides the first transcriptome of an Arctic marine crustacea and reveals first insights into the transcriptomic response of Hyas araneus to changes in ocean acidification and temperature.