Copy number variants (CNVs) are one of the most common forms of genetic variation, both in terms of mutation rate and the proportion of the genome they cover. These variations can significantly affect various phenotypic traits and play a crucial role in the adaptation, health and production traits of animals. The Pag Island sheep is known for its adaptability as well as for its high-quality meat and milk with specific traits such as high milk fat content and fine wool. The objectives of this study were to detect CNVs and CNV regions (CNVRs) in the Pag Island sheep genome that are specific to the population, to map CNVRs to genes and their functions, and to identify QTL regions that overlap with CNVRs. Genotypes (Ovine Infinium® HD SNP BeadChip) of 25 Pag Island sheep and 75 individuals of other breeds (Istrian sheep, Dalmatian Pramenka and Dubrovnik Ruda) were used for the study. Using bioinformatics tools to detect CNVs and functional gene association, a total of 955 CNVRs were discovered, 18 of which were unique to the Pag Island sheep. These regions contain genes critical for traits such as resistance to environmental conditions, nutrient metabolism and reproduction, and are present in biological pathways that provide insights into the genetic basis of the Pag sheep's adaptation to specific environmental conditions. In addition, QTLs associated with wool fineness, milk coagulation traits and meat production have been identified. These findings can make an important contribution to further improvements in breeding programs, optimizing nutrition and achieving higher productivity, thus ensuring the high quality of products such as milk and cheese for which the Pag Island sheep is known.