Small isolated populations often show lower genetic variability. Demographic bottlenecks lead to loss of genetic variation too. Arctic foxes (Vulpes lagopus) have been isolated since the Pleistocene on Mednyi and Bering Islands (Commander Islands). In 1970–1980, the Mednyi population passed through a severe bottleneck due to a mange outbreak. Previous studies showed lack of genetic diversity in the contemporary Mednyi population that could be due to the long history of isolation and/or the recent bottleneck. To test both factors, we analyzed the mtDNA D-loop fragment and five microsatellites in pre-bottleneck Mednyi museum samples. Also, contemporary Mednyi, Bering and mainland Alaskan Arctic foxes were analyzed. Registered genetic variability in historical Mednyi was higher than in contemporary Mednyi Arctic foxes, but lower than in contemporary the Bering population. Our data confirms that the bottleneck reduced an already depleted polymorphism in Mednyi Arctic foxes. Lack of genetic variability could be a reason why the Mednyi population did not recover following the outbreak of mange.