The copepod Calanus finmarchicus plays a crucial role in the north Atlantic food web, channelling energy from phytoplankton primary production to higher trophic levels including commercially important fish stocks like herring and cod. The copepod species is spreading northward into the Arctic due to ocean warming. The activity phase of C. finmarchicus in spring/summer is characterized by diel vertical migration, meaning that the animals migrate to surface waters around sunset to feed, and back to deeper layers around sunrise to hide from visual predators. This rhythmic vertical migration behaviour is characteristic for zooplankton communities all around the world. At the end of the activity phase in autumn, C. finmarchicus enters an overwintering mode and inactively dwell in deep waters until next spring when it starts a new generation cycle. Although both rhythms (diel and seasonal) have been studied for more than a century, the exact factors controlling them are still unclear. Molecular techniques have precisely described genetic clockworks in numerous species and there is clear evidence that clock genes are not only involved in the regulation of diel 24h rhythms, but also in the entrainment of the seasonal cycle. We present first records of clock gene expression in Calanus finmarchicus from a high Arctic fjord in Svalbard at 79°N and compare gene activity between specimen in the early and late phase of overwintering. Copepods were sampled from overwintering depth (>220 m) in September 2014 when surface photoperiod was about 10 hours and during polar night in January 2015 when no light was present. Samples were analysed by quantitative real-time PCR (qRT-PCR) using custom designed Taqman® low-density array cards. The results show clear 24h oscillations in most genes for September, whereas gene expression is almost completely arrhythmic during the polar night in January. It furthermore appears that in September most of the investigated clock genes show distinct expressions patterns, which often match pattern previously observed in other (model) species. For example, expression of period (1 & 2) is highest around sunset (per1) or early night (per2) whereas activity of clock sharply increases around sunrise and peaks in the afternoon. Expression of cryptochrome 1 is highest around midnight while expression of cryptochrome 2 shows patterns similar to those of the period genes. The results strongly point towards the existence of a light-entrained genetic clock in Calanus finmarchicus that becomes arrhythmic during the constant darkness of the polar night. Our work presents an example on how the vast mechanistic knowledge about endogenous timekeeping gained from model organisms can be transferred to field studies on non-model species of high ecological relevance.