We amplified 18S rDNA metabarcodes (the V4 region) from 23 marine planktonic DNA samples to investigate abundance, diversity and depth stratification of eukaryotic microogranisms, primarily those of the Diplonemea group (Excavata). Plankton samples were collected at three locations in the Davis Strait and at eight locations in the Greenland Sea, from surface and from depths of 200, 350, 400, 500, and 1000 m. DNA was isolated from two size fraction: 0.8-20 µm and > 5 µm).