Fédération Cynologique Internationale (FCI) classifies a group of hound dogs in the sixth FCI group divided into three sections and three subsections that include 76 dog breeds. With the Istrian wire-haired hound, the Bosnian broken-haired hound-Barak is one of the two internationally recognized and standardized broken-haired hound breeds from the Balkans. However, genotyping of this breed has not been the subject of study so far. A total of 30 dogs (22 males and eight females) from different breeders from 17 locations in Bosnia and Herzegovina were selected for genotyping. All selected individuals had a valid pedigree issued by the Kennel Club in Bosnia and Herzegovina to ensure dogs were unrelated. Hairs with follicles were used for DNA extraction. Ten microsatellite loci from the commercial StockMarks® for Canine Genotyping Kit were amplified. Estimated genetic indices showed that Bosnian broken-haired hound-Barak harbors a high genetic variability. Phylogenetic relationships between Barak and the other 15 dog breeds, including Tornjak, another indigenous breed from Bosnia and Herzegovina, were assessed. An analysis showed clear differentiation of Barak, with Tornjak as the closest one among analyzed breeds. The results suggest that Barak, as we know it today, was developed during the formation of most modern breeds. Although Barak cannot yet be considered an endangered breed thanks to enthusiasts and hunters, the declining population trends impose the urgent need to establish an animal gene bank and programs for in situ conservation to protect and preserve this autochthonous breed of hound dog for future generations.