The high-latitude Antarctic krill, Euphausia superba, is a key species in the Southern Ocean, a region with extreme seasonal and daily changes in photoperiod (day length), light intensity, sea-ice extent, and food availability. In particular, changes in environmental light regimes have been shown to strongly influence krill circadian clock mechanisms and, by extension, synchronized metabolic or physiological output functions. However, knowledge of clock gene functions and regulations in Antarctic krill is still limited, especially with regard to clock gene products, their distribution, and their impact on oscillatory rhythmicity and chronobiological functions. In particular, it is still unclear whether or not the circadian clock might be functioning in krill during summer and winter, when due to the high latitude krill are exposed to near constant light and near constant darkness respectively. This study aims to provide a first basic insight into clock gene expression in wild Antarctic krill during winter conditions. Besides, methodological optimization was attempted to identify putative tissue-specific rhythmic gene expression patterns in brain and eyestalks. In summary, significant 24 h and 16 h oscillatory rhythms could be identified in the relative gene expression of three important clock genes, Cyc, Sgg, and Tim, as well as in the metabolic gene Atpg in both krill brain and eyestalks. Additionally, nine of ten tested clock genes displayed a general tendency for upregulation in the early night in both tissues during low to even absent light regime. The results of the present study suggest that krill brain and eyestalks are equally important for clock gene expression due to similar detected amplitudes and therefore the analysis of whole krill heads is recommended for further studies. Furthermore, the results suggest that the circadian clock might be still active in wild krill during winter, despite the extremely low levels of day light to which the animals might be exposed. Future investigations concerning the regulation of endogenous timing systems and rhythmic functions in Antarctic krill might help to understand how circadian functions might be preserved during summer and winter at high latitudes and also how these might be affected by potential environmental alternations driven by climate change.