Diatoms are key members of the oceanic phytoplankton and major contributors to global marine primary production and biogeochemical cycles. The family Thalassiosiraceae is a successful and diverse diatom group, which dominates in particular in coastal water. Despite recent ‘omic’ efforts dedicated to diatoms, more reference sequence data are needed to elucidate the molecular mechanisms that enable their success in a wide range of environments. We present ten transcriptomes from species belonging to the genera Thalassiosira and Minidiscus isolated from the English Channel and the Western Antarctic Peninsula. We describe the assembly process, quality evaluation, annotation procedure, and gene expression analysis. The data generated are of high quality, with good assembly and annotation metrics. Similarity analysis shows a clear separation according to environment and species. These data will be of high interest for phytoplankton genomic researchers since it includes the first transcriptomes from Thalassiosiraceae strains isolated from Antarctic waters and the first ones for species of the genus Minidiscus.