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The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the <i>Psychrobacter</i>, <i>Sulfitobacter</i> and <i>Polaribacter</i> genera were dominant in samples from both types of communities. The first type of community was also dominated by members of <i>Halomonas</i>, <i>Pseudoalteromonas</i>, <i>Planococcaceae</i> and an unclassified representative of the <i>Alteromonadaceae</i> family. The second type of community also had a significant proportion of <i>Nitrincolaceae</i>, SAR92, SAR11 Clade I, NS9, <i>Cryomorphaceae</i> and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.