Sea ice is a large and diverse ecosystem inhabited by bacteria and protists contributing significantly to primary production in ice-covered regions. In the Arctic Ocean, sea ice consists of mixed multi-year ice (MYI) and thinner first-year ice (FYI). Due to global warming we experience a shift from MYI towards FYI. Despite the great importance of the sea ice ecosystem, little is known about its functional biodiversity, i.e. which species are actively contributing with which functions to the community. We investigated the eukaryotic biodiversity in MYI and FYI from the central Arctic Ocean using 18S rRNA and rDNA amplicons and compared the “total” biodiversity (rDNA-based) with the “active” biodiversity (rRNA-based). Groups like Ciliophora, Bicosoecida and Bacillariophyceae were over-represented in the active part of the community and grazers appear most active in one FYI station due to the advanced stage of melt compared to the other stations. Furthermore, preliminary results of transcriptomic stress experiments with an abundant naviculoid sea ice diatom show that based on physiological parameters this diatom has a broad thermal range (5 °C to -5 °C) but significantly changes its gene expression pattern at higher temperatures.