Our objective is to contribute and improve the currently available transcriptomic resources for Calanus spp. and explore de novo transcriptome data as an alternative to whole genome sequencing to infer evolutionary relationships within the genus Calanus in the northern seas. Here, we sequenced, assembled, and annotated de novo transcriptomes of two species for the first time (C. hyperboreus and C. marshallae), and three species with some but limited transcriptomic data available (C. glacialis, C. helgolandicus, and C. pacificus). We also investigated hundreds of protein-coding genes from RNA-seq data and update the phylogeny of the genus Calanus.