Continuous light treatment during early juvenile stages in Gadus morhua is a common farming management practice but the effects of these unnatural light conditions on fish stress have received scant attention. In the present study we investigated how continuous illumination affects transcription levels of key stress-related and antimicrobial peptide genes in juvenile Atlantic cod. Gene expression quantification by real-time PCR revealed higher levels of transcripts coding for antioxidant enzymes, namely superoxide dismutase, catalase and glutathione reductase in liver of fish reared under continuous illumination, concomitantly with a 43% decrease in glutathione content. Transcription of antimicrobial peptides such as piscidins, hepcidin and cathelicidin was also affected by constant illumination. Overall, the significant changes in liver transcript levels of these biomarkers in response to continuous light may be an adaptation to light stress.