A change in photoperiod has been implicated in triggering a transition from an active to a quiescent state in Antarctic krill. We examined this process at the molecular level, to identify processes that are affected when passing a photoperiodic threshold. Antarctic krill captured in the austral autumn were divided into two groups and immediately incubated either under a photoperiod of 12 h light:12 h darkness (LD), simulating the natural light cycle, or in continuous darkness (DD), simulating winter. All other conditions were kept identical between incubations. After 7 days of adaptation, krill were sampled every 4 h over a 24 h period and frozen. Total RNA was extracted from the heads and pooled to construct a suppression subtractive hybridisation library. Differentially expressed sequences were identified and annotated into functional categories through database sequence matching. We found a difference in gene expression between LD and DD krill, with LD krill expressing more genes involved in functions such as metabolism, motor activity, protein binding and various other cellular activities. Eleven of these genes were examined further with quantitative polymerase chain reaction analyses, which revealed that expression levels were significantly higher in LD krill. The genes affected by simulated photoperiodic change are consistent with known features of quiescence, such as a slowing of moult rate, a lowering of activity levels and a reduction in metabolic rate. The expression of proteases involved in apolysis, where the old cuticle separates from the epidermis, showed particular sensitivity to photoperiod and point to the mechanism by which moult rate is adjusted seasonally. Our results show that key processes are already responding at the molecular level after just 7 days of exposure to a changed photoperiodic cycle. We propose that krill switch rapidly between active and quiescent states and that the photoperiodic cycle plays a key role in this process. Crown Copyright © 2009.