Protists are single-celled organisms, which are very sensitive to changes in environmental parameters. They show a high diversity and occur under a huge variety of environmental conditions – also in polar regions. They live in and on the ice flows, as well as in the water column beneath. The knowledge about the interchange of marine protists between sea ice and the water surface is still insufficient, whereas more and more studies pay attention to the cryopelagic coupling of these microorganisms. Recently in the context of global change, where sea ice minima are observed more frequently - especially in the Arctic Ocean. The central hypothesis of this thesis refers to the coupling of the protist communities in the sea ice and the water column. During the freezing process, the salt leaves the ice through a channel system (“brine channels”), which contains high salinities and offers many habitats for different organisms to coexist on small scales. Therefore, we assume a higher diversity in the sea ice than in the under-ice water. Although the distance between both habitats is relatively small, results of other studies in the Arctic Ocean showed already differences in the community composition. To address this hypothesis, a molecular approach has been chosen. The protist community in the ice and the water shows a similarity of ~ 60-70%. This result indicates, that the exchange between ice and water is relatively high, which confirms former studies about cryo-pelagic coupling. The second part of this thesis is about the comparison of the cryo-pelagic coupling between the Arctic and the Southern Ocean, to get insides into potentially different mechanisms in both polar regions. Data for the Southern Ocean are still scarce in this context. Therefore, we include Antarctic samples from the equivalent season. A taxonomic overlap of ~ 60-70% between the sea ice and the under-ice water is remarkable. Therefore, we conclude similar mechanisms like in the Arctic Ocean. In total, ~ 60% of the taxa are found in both, the Arctic and the Southern Ocean. Consequently, a global exchange of marine protists is imaginable, but true bipolarity has to be proven by sampling in latitudes between both poles. The focus of the last part is on freshwater taxa and especially the comparison between the land-surrounded Arctic Ocean and the ocean-surrounded Southern Ocean. The Arctic Ocean is influenced by a higher amount of freshwater input (e.g. rivers), and our results confirm more freshwater taxa in the Arctic samples than in the samples of the Southern Ocean. The results of this study bring inside into a variety of aspects of cryo-pelagic coupling in the Arctic and Southern Ocean. The high exchange of taxa between the sea ice and under-ice water, as well as the occurrence of one taxon at both poles, might be more common than assumed by previous studies and need to get more attention in the future, when a further impact of climate change on ice extension takes place.