The data set comprise 25 archived sinking particle samples from moored sediment traps deployed between ~ 80 – 280 m water depth in Fram Strait (Arctic Ocean), which were obtained in the framework of the Long-Term Ecological Research Site HAUSGARTEN and the Helmholtz infrastructure program FRAM. The samples correspond to those obtained during the highest particulate organic carbon (POC) flux in spring and summer, we used the data to investigate variations in eukaryotic community structure over a period of 12 years (2000 – 2012).