This study aimed to identify the genomic differences between the autochthonous Czech pig breed Přeštice Black-Pied and wild boar by screening selection signals distribution in the autosomal genome. Analysis of selection signals was based on the assumption that SNPs extremely related to the population structure can be responsible for biological adaptation. We used genomic data from 265 Přeštice Black-Pied pigs and 75 wild boars collected in Czechia and Slovakia, respectively. Animals were genotyped by two platforms, Illumina Porcine SNP60 and GGP Porcine 50k. After SNP pruning, the database included 30,704 informative autosomal SNP markers. Selection signals were defined by outlier SNPs resulting from the principal component analysis while accounting for population structure. Above the cut-off value set based on the Bonferroni correction were found 234 outliers. Selection signals were distributed in different areas on autosomes 1, 2, 4, 8, 9, and 14.