The peculiarity of the Russian North gene pool has long become scientific fact, but has yet to receive informative explanation. Genetic drift cannot be the only contributing factor in the striking genetic differences between not only northern Russian populations and the southern ones, but among individual northern populations as well. Studying Russian North gene pools previously underrepresented in scientific literature may help understand this phenomenon. The work aimed to perform a subtotal study of the gene pool of the Arkhangelsk Oblast Pomors (Onega Coast, Summer Coast, the western fragment of the Winter Coast; n = 130) using a panel of 60 Y-chromosome SNP markers through multidimensional scaling and mapping of genetic distances. The frequencies of 14 identified haplogroups differ drastically in Pomor populations: haplogroups I1, R1a, and N3 each comprise a quarter of the total Pomor gene pool, I2-P37.2, and R1b each comprise about 8%, and the rest of the haplogroups are rare. The Onega Coast Pomors showed genetic similarity to a wide range of North-Eastern Europe Finnic-speaking populations, as well as to Russian populations with a strong pre-Slavic substratum. The Summer Coast Pomors are close to the Scandinavian gene pools, and the Winter Coast Pomors are similar only to specific Finn and Swede populations. None of the Pomor populations demonstrate genetic similarity with the Novgorod Oblast Russian populations, with which the origin of the Pomors is traditionally associated. The genetic distances between Pomor populations are so great, they are comparable to the general range of variability between the Eastern Slavic, Baltic, and Finno-Ugric peoples of the region. The reasons for such pronounced originality of Pomor populations presumably include, along with genetic drift, the gene pool of each population being underlied by a different pre-Slavic substrate, with later gene flows as an additional factor.