Information on current diversity and biogeography of Arctic marine microbes (bacteria, archaea and single cell eukaryotes) with adequate temporal, spatial and taxonomic resolution is urgently needed to better understand natural dynamics of ecosystem states in space and time, and consequences of environmental change by anthropogenic factors. Here, we introduce a standardized molecular-based observation strategy for high resolution assessment of marine microbes in space and time, even in remote areas such as the Arctic Ocean. The observation strategy involves molecular analyses such as Next Generation Sequencing (NGS) 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 approaches. This includes newly developed automated under-way sampling, moored sediment traps and year-round water samplers, as well as CTD-casts, multi-corers, bottom landers and in the future seafloor crawlers. An integrated standardized dataset including linked, searchable information on synchronous environmental variables provides comprehensive information on the diversity, abundance and biogeography of Arctic marine microbes, covering all three domains of life. The development of the observation strategy involves a set of coordinated pilot studies testing questions of temporal and spatial resolution, i.e. to assess the impact of sea-ice on Arctic marine single-cell eukaroyte community composition, or of ocean warming in Eastern Fram Strait since the year 2000. In the future, the observation strategy for Arctic marine microbes will be implemented as a distributed Molecular Microbial Observatory in the framework of the Arctic observatory FRAM (Frontiers in Arctic Monitoring) and contributes to the ATLANTOS strategy for an integrated Atlantic observatory including genomic information.