The presence of Giardia genotypes was investigated in 18 raccoon dogs (Nyctereutes procyonoides) and 80 red foxes (Vulpes vulpes) on one farm. To demonstrate Giardia cysts, fresh and trichrome stained smears were microscopically screened. Two molecular markers were used for Giardia genotyping: a fragment of the beta-giardin gene and a fragment of the glutamate dehydrogenase gene. All faecal samples obtained from red foxes were negative. Giardia cysts were identified only in 2 of the 18 raccoon dogs. The result of genotyping and phylogenetic analysis showed that the G. duodenalis from both raccoon dogs belonged to the D assemblage. This finding of a new animal reservoir of G. duodenalis canids-specific genotypes is important in order to eliminate the risk of infecting other animals bred for fur. Further molecular analyses of Giardia isolates in raccoon dogs are required. The present study represents the first contribution to knowledge of G. duodenalis genotypes in raccoon dogs.