The Southern Ocean is a region with strong seasonality in sea ice coverage, food supply and photoperiod (the day length). Antarctic krill (Euphausia superba) a key organism in this habitat show remarkable adaptation to this environment by evolving daily and seasonal rhythmicity of physiological and behavioural functions. Recent investigations of these rhythms have demonstrated that an endogenous circadian clock times metabolic output rhythms in krill, synchronized by photoperiod. In krill, the mechanisms of clock genes and their products, however, leading to these rhythms, the distributions of the genes as well as chronobiological functions are essentially unknown. The present study aims for a more comprehensive analysis of endogenous circadian regulation in Antarctic krill, especially with regard to possible optimization of the methodological approach to the identification of putative rhythmic gene expression patterns in brain and eyestalks of krill, in the laboratory. Within this study, were able to demonstrate significant 24h rhythmic oscillation for Cyc and Vri in brain and in general within the eyestalks more pronounced patterns and agreement with literature, could be identified. We further conclude that gene expression probably play the same role in both tissues, except for Dbt. However, we conclude that the analysis of the whole head is more suitable for the future, because amplitudes of the oscillation are the same and only Dbt obtained differences in gene expression within the tissues. Moreover, there is probably first evidence that the interactions between the genes within a tissue might be displaced by a 4 hour rhythm as well as that the transmission between the tissues needs a larger time frame. Further studies in Antarctic krill needs to investigate more knowledge on chronobiological behavior and the associated endogenous timing system, on the contributions of individual clock genes on transcriptional as well as on protein level and on neuroanatomical signal perception and transmission. Key words: Antarctic krill, circadian clock, clock genes, brain and eyestalks, laboratory, relative mRNA level, 12L:12D