During evolution, a wide range of organisms from cyanobacteria to humans have adapted to the day-night cycle, caused by the earth’s rotational movements, by developing an endogenous timing system – a circadian clock – that allows synchronization of metabolism, physiology and behaviour with the environment and that also may modulate seasonal responses. Our current molecular understanding of biological rhythms and clocks is largely restricted to circadian and seasonal rhythms in land model species such as the fruit fly, the mouse or the thale cress. In marine organisms in general, little is known about the principles of endogenous clocks and how these clocks interact with environmental cycles. Marine ecosystems are currently experiencing rapid anthropogenic climatic changes. In particular, polar and sub-polar latitudes comprise the fastest warming regions on the planet with profound impacts on the marine environment. I will outline the importance of this research field in polar regions on the Southern Ocean key species Antarctic krill, Euphausia superba. Our seasonal investigations on krill, both field based and in the laboratory, revealed that important physiological functions such as metabolic activity, feeding and growth, as well as maturity are affected by different light-dark cycles, irrespective of food supply, suggesting that the photoperiod acts as the main Zeitgeber for these annual cycles. In recent investigations we identified an endogenous timing system, which is synchronized by the seasonal cycle of photoperiod, and its link to metabolic key processes. We will further outline the implication of these findings for krill stocks in a changing environment and will present a recently started 5 years project on clocks and rhythms in polar pelagic organisms.