The raccoon dog (Nyctereutes procyonoides) is endemic to East Asia but has been introduced inEurope. Its high adaptability enabled its rapid colonization of European countries, where populationgrowth has been raising concerns regarding ecosystem disturbance and the spread of zoonoticdiseases. The genetic diversity and structure of endemic, source, and introduced populations fromseven locations across South Korea, China, Russian Far East, Finland (spread to Finland afterintroduction to European part of Russia from Russian Far East), Vietnam, and Japan (Honshu andHokkaido) were examined based on 16 microsatellite loci. Two major and significantly different(F ST = 0.236) genetic clusters were found: continental (South Korean, Chinese, Russian, Finnish,and Vietnamese) and island (Japanese) populations. The continental raccoon dog population com-prises three subpopulations (Chinese_Russian_Finnish, South Korean, and Vietnamese) and theJapanese population consists of Honshu and Hokkaido subpopulations. The genetic diversity andgeographic structure of raccoon dogs in East Asia has been influenced by natural barriers to geneflow and reveals a typical central-marginal trend in genetic diversity (continental vs. island, andcentral vs. marginal or source vs. introduced within continental populations). The detected differ-ences between continental and island populations agree with those reported in previous studiesthat considered these populations as different species.