In 2009 scientists at the Alfred Wegener Institute (AWI) Helmholtz Centre of Polar and Marine Research in Bremerhaven established the PEBCAO-group. Since then the group is investigating the “Plankton Ecology and Biogeochemistry in the Changing Arctic Ocean” in a uniquely synchronized approach. This involves the integration of molecular genetic investigations with traditional plankton investigations, optical parameters, microbiology, work on key species (e.g. Phaeocystis sp. or Calanus sp.), and finally the composition of organic matter. The work is carried out in the Central Arctic Ocean and the Fram Strait, where it is complementing a monitoring program on phytoplankton and vertical particle flux that has been carried out along ~79°N and in the AWI HAUSGARTEN for more than ten years. This is done in cooperation with oceanographers and deep-sea biologists. Combining the long-term data (1998-2012) with the integrative approach of PEBCAO we revealed a trend towards slightly higher chlorophyll a in the WSC during summer that is accompanied by a shift from diatoms to Phaeocystis sp. and other small pico- and nanoplankton. Furthermore, a clear zonation in the waters of the East Greenland Current (EGC), the West Spitsbergen Current (WSC) as well as for the mixing zone of both (MW) was identified in all parameters. The PEBCAO approach is an example for a successful and synergistic integration of molecular biodiversity studies with classical approaches of biological oceanography.