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A rapid increase in global annual temperatures leads to decreasing ice cover, causing many ecosystem effects including Arctic and sub-Arctic species range shifts. Killer whales are increasing their presence in the Arctic following ice cover loss. The impact of killer whales on marine ecosystems differs dramatically depending on ecotype: ‘resident’ R-type killer whales feed mainly on fish, while ‘transient’ T-type whales feed mostly on marine mammals. We examined the distribution and genetic diversity of R- and T-type killer whales in the western North Pacific in order to gain insight into their range shifts during and after the Last Glacial Maximum (LGM) and to predict the potential effects of climate change on their range. R-type whales prevail in the coastal waters of eastern Kamchatka, Commander and Kuril Islands and in the central Okhotsk Sea, where deep waters occur close to shore. In contrast, T-type whales dominate the coastal waters of Chukotka and Okhotsk Sea, represented by wide shallows covered with ice in winter. The diversity of the complete mitochondrial haplotypes of both R- and T-type killer whales was lower in the western North Pacific than in the Aleutian Islands and the eastern North Pacific, suggesting the founder effect. We hypothesize that during the LGM killer whales were driven from the western North Pacific by unfavorable ice conditions, and re-colonized it later. This suggests that North Pacific killer whales avoid ice-covered areas but can re-colonize them soon after the ice retreats. Habitat preferences provide an indication that range expansion in the Arctic will likely involve mostly T-type killer whales and consequently increase the predation pressure on marine mammals to a greater extent than on fish stocks. This should be considered in further studies and prediction models highlighting Arctic marine ecosystem change, which is relevant to management of marine protected areas (MPAs).