Due to the high sensitivity of zooplankton to environmental fluctuations, monitoring their taxonomic composition, abundance and biomass is of high priority to identify changes in the ecosystem. Recent advances in imaging and molecular technologies promise to greatly accelerate the processing of samples to determine both the diversity and quantity of the zooplankton community. In our study, we analyzed the diversity and quantity of an epipelagic Arctic zooplankton community using multi-marker metabarcoding and imaging analysis (ZooScan). We identified a total of 11 phyla and 58 species in the northern Barents Sea and the Nansen Basin. Metabarcoding identified more taxa than image analysis, while imaging provided quantitative information on abundance and biomass. Multivariate analyses revealed overall the same significant environmental drivers (temperature and percentage of Polar Surface Water in the sampling depth layer) explaining the similarity and spatial distribution of the zooplankton community. For all approaches, similar spatial patterns of the zooplankton community were found. Abundance, biovolume and biomass decreased with increasing latitude within the analyzed regions. Based on this study, we recommend ZooScan image analysis in combination with COI metabarcoding for future monitoring of Arctic zooplankton diversity and quantification to ensure the detection of changes in both aspects of these communities.