Melanin pigments color the integument of vertebrates with shades of rufous, gray, and black. In numerous wild species, melanin-based coloration associates to different behavioral, physiological, and morphological traits, yet the proximate basis of such associations remains largely unknown. The neural crest/domestication syndrome hypothesis (Wilkins et al., 2014) proposes that correlated changes in pigmentary, behavioral, physiological, and morphological traits of domestic species result from deficiencies affecting the number or development of neural crest cells in the embryo. Here, we review to what extent the neural crest cells might also explain the associations observed between melanin-based coloration and distinct traits in wild vertebrate populations. Genes involved in the development of the neural crest explain color differences in some vertebrate species, particularly, in cichlid fishes. Cells that originate from the embryo's neural crest cells play functions that have been previously associated with melanin-based coloration in wild vertebrates and we propose the potential mechanisms through which the association of melanin-based coloration with other traits can be the consequence of having a common origin at the neural crest cells. We encourage considering the influence of the neural crest as a new avenue of research, integrating developmental biology and evolutionary ecology to better understand why and how melanin-based coloration of vertebrates become associated to multiple phenotypic aspects.