Diatoms are a group of eukaryotic microalgae populating almost all aquatic and wet environments. Their abundance and species diversity make these organisms significant contributors to biogeochemical cycles and important components of aquatic ecosystems. Although significant progress has been made in studies of Diatoms (Bacillariophyta) over the last two decades, since the spread of "omics" technologies, our current knowledge of the molecular processes and gene regulatory networks that facilitate environmental adaptation remain incomplete. Here, we present a transcriptome analysis of Fragilaria radians isolated from Lake Baikal. The resulting assembly contains 27,446 transcripts encoding 21,996 putative proteins. The transcriptome assembly and annotation were coupled with quantitative experiments to search for differentially expressed transcripts between (i) exponential growth phase and dark-acclimated cell cultures, and (ii) those changing expression level during the early response to light treatment in dark-acclimated cells. The availability of F. radians genome and transcriptome data provides the basis for future targeted studies of this species. Furthermore, our results extend taxonomic and environmental sampling of Bacillariophyta, opening new opportunities for comparative omics-driven surveys.