Mammalian color patterns are among the most conspicuous characters found in nature and can have a profound impact on fitness. However, little is known about the mechanisms underlying their formation and subsequent evolution. We capitalized on the naturally occurring color pattern of the African striped mouse, Rhabdomys pumilio, to investigate the formation of periodic stripes, a common pattern in mammals. In striped mice, stripes result from underlying differences in melanocyte maturation, which give rise to spatial variation in hair color. Through transcriptomic analyses of the developing skin, we identified the transcription factor Alx3 as a major hierarchical regulator. During striped mouse embryogenesis, patterned expression of Alx3 precedes pigment stripes and acts to directly repress Mitf, a master regulator of melanocyte differentiation. Moreover, Alx3 is also differentially expressed in the dorsal stripes of chipmunks, which have independently evolved a similar color pattern. Thus, differences in the spatial control of Alx3 lead to striped patterns in rodents, revealing both a new factor regulating pigment cells and a previously unappreciated mechanism for modulating hair color. I’ll end by discussing how my lab, through a variety of multidisciplinary approaches, uses the mammalian skin as a model to uncover molecular mechanisms of phenotypic diversity.