The data has been collected during the year-long drift expedition "Multidisciplinary drifting Observatory for the Study of Arctic Climate" (MOSAiC) from September 2019 to September 2020 on research vessel Polarstern. The dataset contains abundance of pelagic marine and sea ice protists, including algae (autotrophic) and protzoa (heterotrophic). Protists were identified and counted with light microscopy using the Utermöhl method and the result are given as cells per liter (cells/L) called Abundance. The samples were collected with short-term sediment traps deployed at 3-4 depths (1, 5, 15 and 50 m) below level ice and near sea-ice ridges. The samples were preserved with a few drops of Lugol and hexamethylenetetramine-buffered formalin at a final concentrations of 1%.