The western capercaillie is a relict species of birds with cryptic population structure that is located in the highest mountain ranges of western, central, and south-eastern Europe. This thesis discusses genetic structure of the western capercaillie (Tetrao urogallus rudolfi) population in Bulgaria. This species is recognized as an evolutionary significant unit (ESU) due to its isolation, phylogenetic affinity with the southern line, evolutional uniqueness and ability to adapt to different environmental conditions in the past. This recognition emphasizes the need to study and protect the unit. In this thesis, we analyzed 108 individual genotypes of the western capercaillie by using non-invasive samples (droppings, feathers) which were collected between the years 2015 and 2017. These samples came from different localities in the Rhodope, Pirin and Rila mountains. The most favourable situation closest to panmictic population was found in Rhodope Mountains. This population was marked as the source population of the western capercaillie in Bulgaria. The population in the Rhodopes is genetically different from the ones in Pirin and Rila mountains. This difference indicates possible existence of barriers in the gene flow, which makes the populations vulnerable. It is necessary to determine migration corridors and focus on their protections as well as protection of the already existing biotopes. Ensuring long-term existence of the population is possible only by functional connectivity and stopping its decline.