Unlike Oceanic islands, the islands of the Arctic Sea are not completely isolated from migration by terrestrial vertebrates. The pack ice connects many Arctic Sea islands to the mainland during winter months. The Arctic fox (Alopex lagopus), which has a circumpolar distribution, populates numerous islands in the Arctic Sea. In this study, we used genetic data from 20 different populations, spanning the entire distribution of the Arctic fox, to identify barriers to dispersal. Specifically, we considered geographical distance, occurrence of sea ice, winter temperature, ecotype, and the presence of red fox and polar bear as nonexclusive factors that influence the dispersal behaviour of individuals. Using distance-based redundancy analysis and the BIOENV procedure, we showed that occurrence of sea ice is the key predictor and explained 40–60% of the genetic distance among populations. In addition, our analysis identified the Commander and Pribilof Islands Arctic populations as genetically unique suggesting they deserve special attention from a conservation perspective.