Our molecular based observation strategy involves cutting edge molecular analyses such as Next Generation Sequencing (NGS), nucleic acid sensors, analyses of molecular fingerprints and quantitative polymerase chain reaction (qPCR) of diverse environmental samples, collected from sea ice, water column and seafloor with a complementary set of automated and ship-based sampling and analyses approaches. Sampling for the molecular analyses is based on a newly developed automated under-way sampling device, moored sediment traps, as well as CTD-casts. Currently, we are in the implementation phase of the observation strategy with the aim to introduce a standardized molecular-based observation strategy for high resolution assessment of marine eukaryotic microbes in space and time in the near future. This involves development and optimization of sampling technology, establishment and comprehensive evaluation of latest molecular methods for microbial biodiversity assessment at all steps of the analyses.