Mesozooplankton play an important role in Arctic shelf ecosystems as a trophic link and a key food source for many larval fish species. The distribution of mesozooplankton in the eastern Barents Sea was studied along a 500 nautical mile-long transect in May 2016 during the spring bloom. Mesozooplankton were sampled using a Juday net hauled from the surface to the bottom at 12 stations. We found good correspondence between the distribution of water masses and mesozooplankton assemblages. Mesozooplankton abundance (mean 73·103 individuals m−2) in Novaya Zemlya coastal water was dominated by Copepoda ova and nauplii, Thyssanoessa spp. nauplii and Oithona similis. Parasagitta elegans and Calanus finmarchicus comprised most of the total mesozooplankton biomass (mean 0.9 g dry mass m−2) in that water mass. A second assemblage (mean abundance 171·103 individuals m−2) was associated with the colder Barents Sea water, with Oithona similis, Copepoda nauplii, Fritillaria borealis and Cirripedia nauplii being the most numerous. In that water mass, C. finmarchicus, Metridia longa, Cirripedia nauplii and Calanus glacialis contributed most to the total biomass (mean 3 g dry mass m−2). The dominance of young stages of Copepoda and a high proportion of meroplankton were typical of spring mesozooplankton assemblages. The spatial distribution of mesozooplankton abundance and biomass was strongly correlated with latitude, longitude and chlorophyll a concentration, which together explained 10% of the total variance in mesozooplankton density. The present investigation is a baseline study for the assessment of the spring mesozooplankton assemblage in the eastern Barents Sea, and for an evaluation of the possible impact of future environmental changes on the Arctic shelf marine ecosystem.