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The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study has been to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed according to HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound dog: Barak, n=34; Bulgarian Scenthound dog: Gonche, n=45) as well as from a Bulgarian Shepherd dog (n=51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades – A, B, C and D – in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of the C clade, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial diversity of native dog breeds in Bulgaria. The results show a clear difference of haplogroups dissemination in native hunting and shepherd dogs that suggests a dual independent phylogenetic origin without hybridization events between them.