The sea ice structure of the Arctic Ocean has changed measurably in the last decades. Sea ice decline and warming of the surface water layers may affect composition and diversity of protist communities living in the sea ice interface and the pelagic realm. Samples from different habitats were analyzed (1) to investigate the impact of sea ice on the protists and, (2) to elucidate cryo-pelagic coupling. Samples were collected from melt ponds, sea ice, under-ice water and water column during two RV Polarstern cruises to the Central Arctic Ocean in August - September 2011 & 2012. Automated ribosomal intergenic spacer analysis (ARISA) from 182 samples and Illumina-sequencing of 57 samples revealed a high heterogeneity between different melt pond and sea ice samples, whereas samples from the water column were more homogeneous. However, different sea ice habitats showed similar patterns in protist community structure at the same station, indicating intensive sea-ice-water-exchange during melting and freezing processes. These results illustrate that the high biodiversity in the Central Arctic is mainly governed by the sea ice origin compared to the oceanic currents.