The Arctic Ocean is quite vulnerable and sensitive to climatic changes and has received increasing attention in recent years because of the drastic decrease of sea ice cover and extent. These environmental changes are expected to have severe consequences for the structure of the pelagic system and trophic interactions, and thus for cycling of organic matter and carbon sequestering. The composition of particulate organic matter is measured at the so-called ‘HAUSGARTEN’ – a deep-sea long-term observatory of the AWI, in order to track respective shifts. The observatory is situated in the eastern Fram Strait at ~ 79°N and 4°E. Since 1998, yearly sampling has been carried out in the water column during cruises in summer, and sedimenting particles are collected by year-round moored sediment traps. Here we present results obtained from water samples collected near the central station at the HAUSGARTEN during expeditions with RV Polarstern in 1998, 2003, 2004, 2006, 2007, 2009 and 2010. The composition of the dominant groups of phytoplankton and protozooplankton in the upper 100m was investigated qualitatively as well as quantitatively by light microscopy. This time-series enables us to trace possible changes in relation to environmental factors such as temperature, salinity and sea ice cover. Diatoms dominated the phytoplankton in the years 1998 and 2003. These years were characterized by longer periods of sea ice cover and relatively cold water temperatures. Coccolithophorids, mainly composed of Emiliania huxleyi, prevailed in the samples from 2004. During the following years until 2010, which had a low presence or complete absence of sea ice, phytoplankton was dominated by the prymnesiophyte Phaeocystis pouchetii. Concomitant to the shift in phytoplankton composition, we also noted an increase in protozooplankton abundance (ciliates and tintinnids) in the samples. The observed changes in the species composition of unicellular protistian plankton is also partly reflected in the composition of sedimenting matter at the central HAUSGARTEN mooring, indicating just as well modifications in element cycling in the changing Arctic Ocean.