Goat milk's medicinal properties and potential cosmetic and health benefits have prompted extensive scientific investigation into its therapeutic applications, particularly for human skin conditions like eczema and psoriasis. Genetic factors, including genes such as lactoferrin (LTF), lysozyme (LYZ), and β-casein (CSN2), play a crucial role in shaping milk composition and its effects on skin health. This review explores the utilization of genomic tools to elucidate the genomic profiles of dairy goat breeds and the medicinal properties of goat milk, particularly in addressing key skin diseases. Genetic determinants of milk composition, quality, nutritional quality, and functional properties such as the growth hormone receptor (GHR), butyrophilin (BTN1A1) and lactoglobulin (LGB) genes, facilitating targeted breeding strategies to enhance the production of bioactive compounds with dermatological relevance have been identified. Future genomic approaches should aim at exploring goat milk's immunomodulatory, antimicrobial, and antioxidant activities, offering potential applications in skin care formulations for managing inflammatory skin conditions. Furthermore, the integration of genomic data with functional studies can provide valuable insights into the therapeutic effects of goat’s milk and its derivatives in addressing skin diseases.