Single-nucleotide polymorphism (SNP) markers are genetic markers in which a single nucleotidevariation occurs at a specific position in the genome. Characterized by their high abundance, density, and easy genotyping,SNP markers have been widely used in animal and plant breeding, as disease resistance markers, and for the screening ofheterosis and identification of disease-related genes. In the present paper, we first present the application of SNP arrays foranalyzing animal population genetic structure, genetic mapping, and for characterizing marker-assisted selection, kinship,and heterosis. Second, we describe the relationship between SNP loci and animal models of human diseases, which canprovide a valuable reference for the improved application of SNP molecular marker technology in animal genetic breeding,and the establishment and genetic analysis of animal models of human diseases.