The raccoon dog was introduced from eastern to western Eurasia, and subsequently spread throughout Europe all the way to the middle part of Finland, potentially assisted by its high genetic diversity. To elucidate the genetic diversity of Finnish raccoon dogs and its association with resistance to pathogens, we genotyped 77 individuals for ten neutral and eight MHC-linked microsatellite loci, and sequenced MHC class II DRB alleles for 20 individuals. We compared the results with the data from a Japanese population, and detected no differences in the microsatellite variation between these two populations. By contrast, diversity at DRB loci was lower in the Finnish population as compared with that in the Japanese population. No spatial genetic structure was found in Finland, but our analyses revealed two sympatric genetic clusters. The analysed genetic markers did not show associations with the frequency of infection by pathogens such as Trichinella spp.