Changing environmental conditions cause poleward distribution shifts in many marine organisms including the northern Atlantic key zooplankton species Calanus finmarchicus. The copepod has diel cycles of vertical migration and feeding, a seasonal life cycle with diapause in winter and a functioning circadian clock. Endogenous clock mechanisms control various aspects of rhythmic life and are heavily influenced by environmental light conditions. Here we explore how the extreme seasonal change in photoperiod (day length) in a high Arctic fjord affects circadian clock functioning as well as diel and seasonal cycles in C. finmarchicus. Expression of clock genes was measured in the active life phase at the end of midnight sun, in early diapause when photoperiod was ~12 h, and in late diapause during the polar night. While the clock maintained diel rhythmicity under extremely long photoperiods, it became arrhythmic during diapause. This was probably not due to a lack of light but was related to the physiological state of diapause. Seasonal expression analyses of 35 genes show distinct patterns for each investigated life phase. C. finmarchicus is able to maintain diel clock rhythmicity at photoperiods close to 24 h, and it is discussed how this may be related to the nature of the marine environment. The work also evaluates the potential negative consequences of rigid clock-based seasonal timing in a polar environment exposed to climate change and with high interannual variability.