Balkan Livestock Guardian Dogs (LGD) were bred to help protect sheep flocks in sparsely populated, remote mountainous areas in the Balkans. The aim of this study was genomic characterization (107,403 autosomal SNPs) of the three LGD breeds from the Balkans (Karst Shepherd, Sharplanina Dog and Tornjak). Our analyses were performed on 44 dogs representing three Balkan LGD breeds, as well as on publicly available 79 genotypes representing other eight LGD breeds, 70 individuals representing seven popular breeds, and 18 grey wolves. The results of multivariate, phylogenetic, clustering (STRUCTURE), and FST differentiation analyses showed that the three Balkan LGD breeds are genetically distinct populations. While Sharplanina Dog and Tornjak are closely related to other LGD breeds, Karst Shepherd is a slightly genetically distinct population with estimated influence from German Shepard (Tree-mix analysis). Estimated genomic diversity was high with low inbreeding in Sharplanina Dog (Ho=0.315, He=0.315 and FROH>2Mb=0.020) and Tornjak (Ho=0.301, He=0.301 and FROH>2Mb=0.033) breeds. Low diversity and high inbreeding were estimated in Karst Shepherd (Ho=0.241, He=0.222 and FROH>2Mb=0.087), indicating the need for proper diversity management. The obtained results will help in conservation management of Balkan LGD dogs as an essential part of the specific grazing bio-cultural system and its sustainable maintenance.