Planktonic foraminifera cells and water samples were collected in the Baffin Bay during the MSM66 cruise (August 2017). For assessing the pelagic eukaryotic community composition, seawater (1 L) from Niskin bottles was sampled from two sites in the North Ban Bay (GeoB22323-3 and GeoB22333-2) and two sites from the south of the Ban Bay (GeoB22365-3 and GeoB22304-2 at the surface (~5 m) and at depth (200 m) and filtered through 0.2 µm cellulose filters.Planktonic foraminifera specimens collected from different depths at one of the sites in the north, GeoB22333-2 (sampling intervals: 0–20 m, n = 4 150–200 m, n = 15), and from one in the south, GeoB22365-3 (sampling intervals: 0– 30 m, n = 7 120–150 m, n = 13), were selected for single-cell metabarcoding analyses.Samples were then amplified in triplicates using the universal Eukaryotic V4 tagged primers TAReuk454FWD1 and TAReukREV3. Samples triplicates were loaded in four different pools with each unique tagged primer combination present only once in each pool. Pools were sent to the University of Geneva for sequencing Illumina (MiSeq), where sequencing libraries were prepared using the reagents of the PCR-free TruSeq kit (Illumina).