Simple SummaryMink (Neovison vison) is well-known as one of the most important sources of fur and is used as feed across the North zone of China. Using double-digest restriction site-associated DNA sequencing, this study evaluated the genetic diversity and population structure of a five color of mink populations in China (ddRAD-seq). The black mink population was found to be genetically differentiated from other color type populations, whereas a clustering of the red mink and black mink populations was observed; further, other color populations clustered separately. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the genes with a selection signature were enriched in the melanogenesis pathway. The results of our study provide basic information on mink diversity, and theoretical concepts for the conservation and exploitation of mink breeds in China.AbstractThe American mink (Neovison vison) is a semiaquatic species of Mustelid native to North America that is now widespread in China. However, the knowledge of genetic diversity of mink in China is still limited. In this study, we investigated the genetic diversity and identified significant single nucleotide polymorphisms (SNPs) in mink populations of five different color types in three different mink farms in China. Using double-digest restriction site-associated DNA sequencing, we identified a total of 1.3 million SNPs. After filtering the SNPs, phylogenetic tree, Fst, principal component, and population structure analyses were performed. The results demonstrated that red mink and black mink grouped, with separate clustering of all other color types. The population divergence index (Fst) study confirmed that different mink populations were distinct (K = 4). Two populations with different coat colors were subjected to the selection signature analysis, and 2300 genes were found to have a clear selection signature. The genes with a selection signature were subjected to Gene Ontology (GO) categorization and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the results revealed that the genes with a selection signature were enriched in the melanogenesis pathway. These study’s findings have set the stage for improved breeding and conservation of genetic resources in real-world practical mink farming.