Every day we witness the reduction of genetic variability of plants and animals. The extinction of animals is a process that is constantly taking place, and the loss of genetic material is inevitable. As we intensify selection for higher production, we reduce the genetic variability of these species. Autochthonous animals are usually lower production animals raised in extensive systems and are better adapted to environmental conditions and therefore have higher genetic variability. Sheep breeding has historically been an important part of agricultural production on Croatian territory. It is believed that sheep came to Croatia with human migrations in the Neolithic period and are an integral part of Croatian culture since. In the 18th century, Dalmatia had the highest number of sheep in Europe. Since then, the number of sheep has steadily decreased and some of the Croatian sheep breeds are threatened with extinction. The Croatian autochthonous sheep breeds are low production animals adapted to harsh environmental conditions and extensive breeding systems. They all belong to the Pramneka sheep type or are descended from the Pramenka sheep type. There are nine recognised autochthonous sheep breeds in Croatia and eight of them are discussed in this doctoral thesis: Istrian sheep, Cres Island sheep, Krk Island sheep, Pag Island sheep, Rab Island sheep, Dalmatian Pramenka, Lika Pramenka and Dubrovnik sheep -ruda. Another 21 European sheep breeds from the Data repository were included in this analysis as well as ten mouflon samples from Kalifront. This PhD aimed to estimate the conservation status of Croatian autochthonous sheep breeds, determine the unique parts of the genome and position Croatian autochthonous sheep breeds in the Mediterranean context. For this purpose, the high-density Infinium Ovine HD SNP chip was used, which contains 606 000 polymorphic positions. All Croatian autochthonous sheep breeds were successfully genotyped. Croatian autochthonous sheep breeds showed high genetic diversity. Based on the analysis within and between populations, it is clear that Croatian autochthonous sheep breeds are divided into two groups based on their geographical characteristics: island breeds and continental breeds. Island breeds include Istrian sheep, Krk Island sheep, Cres Island sheep, Rab Island sheep and Pag Island sheep, while continental breeds include Lika Pramenka, Dalmatian Pramenka and Dubrovnik sheep. This clustering was confirmed with PCA, Structure analysis, Nei distances represented with Neighbour Net network and phylogenetic analysis performed with SplitsTree. Furthermore, the Structure analysis showed that not all breeds are completely separated. The Pag Island sheep and the Rab Island sheep, as well as the Lika Pramenka and the Dalmatian Pramenka, showed similar ancestral breed composition, indicating greater genetic relatedness. The Croatian autochthonous sheep breeds showed a lower degree of genomic inbreeding obtained from runs of homozygosity. The highest inbreeding was observed in Dubrovnik sheep with FROH > 2Mb = 0.07. Higher recent inbreeding (up to 5 generations ago) was observed in all breeds. The lowest effective population size was observed in sheep from the island of Krk (61), but lower Ne was also observed in sheep from the island of Cres (148), Dubrovnik sheep (157) and Istrian sheep (161). The highest effective population size was observed in Dalmatian Pramenka sheep (1039). The Croatian autochthonous sheep breeds observed in the Mediterranean context grouped with other European Pramenka sheep types. In the PCA diagram, they were placed in the middle of the diagram, creating a link between Eastern European and Western European sheep breeds. The Croatian autochthonous sheep breeds had eight specific genomic regions compared to the European breeds. Since some of the Croatian autochthonous sheep breeds have lower effective population size and higher inbreeding, additional caution should be taken when implementing breeding programmes.