The accelerated loss of annual sea ice in the Arctic Ocean due to global warming imposes changes of unknown consequences upon bacterial community structure, not only in sea ice but also in seawater. Using highly parallel tag-sequencing of the V4 region of the 16S rRNA gene, we characterized the bacterial community (structure and composition) at unprecedented spatial resolution in sea brine (water collected from the channels within the ice) and surface seawater in the Arctic Eurasian Basin. Onboard IBRV Oden, we analyzed 12 open ocean, ice-covered stations, crossing the North Pole during summer 2012, recording also values of salinity, temperature, nutrient concentration, and pigments.