The Fram Strait separates Northeast Greenland from the Svalbard Archipelago, and is the only deep connection to the Arctic Ocean. Therefore, this strait is the only gateway for direct exchange of intermediate and deep waters between the Arctic Ocean and the North Atlantic. Two main currents influence the exchanges: i) the West Spitsbergen Current, bringing Atlantic waters northwards, and ii) the East Greenland Current, which carries cold Arctic waters and ice southwards. These two currents consist of water masses with different origin, generate distinct physical and chemical conditions between the eastern and western parts of the strait, which effects the biological characteristics in this region. Oceanographic observations in the Fram Strait have been carried out for ~15 years with microbial research in the water column focusing mainly on eukaryotes, while very little exploratory work was conducted on pelagic Bacteria and Archaea. Here we present a preliminary report of the first extensive survey across the waters of the Fram Strait focused on Bacterial and Archaeal domains, conducted as part of the Arctic long-term observatory HAUSGARTEN annual expedition in summer 2016. Besides the investigation of “who is out there”, the observations gained in this survey will be integrated with other biological and physical data of the long-term observatory framework and will provide an essential step towards the understanding of the biochemical dynamics in the Fram Strait. In addition, on a long-term plan this project will contribute to the microbial observatory work as part of the FRAM Helmholtz research infrastructure and EU AtlantOS program.