Mammalian coat color is one of the first phenotypic changes resulting from positive selection by humans, and it serves important roles in genetic and evolutionary processes. Among them, horses show a broad variety of coat color patterns, based on which it is difficult to distinguish the real phenotypes, resulting in confused records in horse breed registration. Thus, research in the genetic mechanisms on the development of coat color patterns is significant in horse reproduction and breeding. With the recent establishment of genomics and sequencing technologies, there are significant advances in research in the genetics of horse coat colors, which demonstrate that special coat colors could be associated with certain diseases. In this review, we classify horse coat colors from the perspective of genetics, and summarize the recent research progresses of the associated genes and molecular mechanisms on horse coat color development and its application, thereby providing references to further systematic research on horse coat color patterns and their practical uses in horse breeding.