Abstract Only a few historical assessments of the zooplankton biomass in the Arctic Ocean exist are difficult to compare due to methodological differences including incomplete sampling of the water column. We present assessments of the zooplankton biomass for 66 locations scattered over the Eurasian and Makarov Basins of the Arctic Ocean and analyze regional variability and factors affecting the biomass distribution. The study is based on material from several summer expeditions of RV Polarstern (1993–1998) that was collected and processed using consistent methods, i.e. stratified sampling of the entire water column from the bottom to the surface with very similar gear and standardized calculation of biomass. Total zooplankton biomass varied strongly from 1.9 to 23.9 g DW m −2 dry mass. Regional variability was mainly related to the circulation pattern, but local food availability was also important. A belt of elevated biomass along the Eurasian continental margin was associated with the advection of Atlantic pelagic populations within the Arctic Ocean Boundary Current along the Siberian shelves and returning branches along mid-ocean ridges. Biomass was highest in the core of the Atlantic inflow and remained rather stable along the continental margins, but species composition changed, pointing to different adaptation levels to local conditions by advected species. Biomass gradually decreased towards the shelves and basins and was lowest in the centers of the basins north of 85°N. In the slope region, three Calanus species ( C. hyperboreus, C. glacialis, C. finmarchicus) and Metridia longa contributed most to the biomass, chaetognaths ( Eukrohnia hamata) were also important. In the basins, C. hyperboreus was dominant, copepods made up to 97% of total biomass. Vertical distribution was similar at all stations with biomass maxima in the upper 50 m layer except for stations near Fram Strait and northern Kara Sea, the gateways of Atlantic water to the Arctic Ocean, where maxima where between 25 and 100 m. As there was only very little interannual variability of temperature and current velocity in the regions of the Atlantic inflow we suggest that the majority of our samples, collected in 1993 and 1995, represents the phase of the 1990s warm event in the Nordic Seas.