We studied the epigenetic variability and epigenetic distance of raccoon dogs from seven European localities and the species' Amursk area of origin. The studies were based on 24 non-metric traits in 1046 skulls. Native raccoon dogs from the Amursk region showed the same low level of epigenetic variability as the European populations, giving no indication of a founder effect or inbreeding. Epigenetic distances between raccoon-dog populations were generally high. The German regions formed a separate cluster with a rather high epigenetic distance to the Finnish-Polish group. This indicates different migration lines of the species. The native raccoon dogs of the Amursk region were completely separate from the European populations as a consequence of the distinct reproductive isolation of about 60 years, as well as an effect of the colonisation and migration history of the species.