Sea ice is a large environment controlled by a number of abiotic factors (i.e. low temperatures and high salinities). Despite these harsh conditions, it is inhabited by a diverse community and significantly contributing to primary production in ice-covered regions. While this biodiversity has been investigated in the past by classical methods, little is known about its functional biodiversity, i.e. which species are actively contributing with which functions to the community. By sequencing 18S rRNA and rDNA amplicons, we were able to compare the “total” biodiversity (rDNA-based) with the “active” biodiversity (rRNA-based) and found an over-representation of certain groups (i.e. Bacillariophyceae and Ciliophora) in the active part of the community. Furthermore, we were able to isolate an abundant naviculoid sea ice diatom member (CCMP2297) of the Arctic sea ice community and conducted temperature stress experiments (10 °C, 5 °C, -2 °C, -5 °C) and analyzed not only physiological responses to high and cold temperature stress, but also the molecular responses to thermal stress by sequencing the transcriptome. We found 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.