Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation ( ) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color ( ), salivary secretion ( ), reproduction ( , , , , and ), olfactory transduction ( ), and growth ( , , and ). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production.