Samples were collected during the Polarstern cruise PS112 between March and May 2018 along the western Antarctic Peninsula in the Southern Ocean. Genomic DNA was isolated from filtered water samples (0.4µm), the stomach content of freshly caught Antarctic krill (Euphausia superba) and salps (Salpa thompsoni), as well as from their faecal pellets. A 452bp long fragment of variable region V4 of the 18S rRNA was amplified and sequenced using a MiSeq Illumina platform in 2x300 bp paired-end runs.