The psychrophilic pennate diatom Fragilariopsis cylindrus is a dominant polar diatom adapted to grow at extremely low temperatures and high salinities prevailing in the brine channels of sea ice. As a basis for deeper investigations of this physiological trait, we used an EST approach to find candidate genes involved in acclimation to salt stress in this diatom. From 2880 cDNA clones sequenced from the 5′ end, 1691 high-quality tentative unique sequences were assembled and analysed. Only 62% of these sequences have homologues in the genomes of two mesophilic diatoms, Thalassiosira pseudonana (centric) and Phaeodactylum tricornutum (pennate), which share 73–78% of their genes. Of the 1691 sequences, 44.2% could be functionally characterized by comparison with the Swiss-Prot and RefSeq databases. These include sequences encoding different ionic transporters and antiporters, reflecting the requirement to re-establish the ion homeostasis disturbed by exogenous salt stress. Furthermore, numerous genes encoding heat shock proteins (hsps), genes related to oxidative stress, and three key genes involved in the proline synthesis pathway, the most important organic osmolyte synthesized in F. cylindrus were identified. A major outcome of this analysis is the finding of four full-length ORFs showing significant similarities to ice-binding proteins (IBPs), which have been shown in a parallel study to be specific to sea ice diatoms, giving evidence of their ability to shape their habitat.