Horses were domesticated 5500 years ago, thousands of years later than other domestic animals; however, in this relatively short period, domestic horses have had a great impact on human history by accelerating civilization, revolutionizing warfare and advancing agricultural production. Modern breeding using marker-assisted selection has greatly accelerated breeding progress. Therefore, identification of genetic markers underlying the traits of interest in domestic horses is the basis for the modern breeding system. In this review, we present an overview of genetic mapping studies and genome wide analyses to identify the genomic regions targeted by positive selection for four important aspects of horses, coat color, racing performance, gait and height at withers. The locus, for example, has been shown to be the main gene responsible for chestnut color, and the locus has been shown to control the muscle fiber growth in racing breeds. The missense mutation in is the causal mutation for the alternate gaits in horses. Height at withers, a quantitative trait, was mapped to four major loci (3:105547002, 6:81481064, 9:75550059 and 11:232597 32) that can explain 83% of the height variations in domestic horses.