Color is a key biological trait that allows individuals to adapt to their biotic and abiotic environment, and many genes have been shown to play an essential role in color acquisition in vertebrates. In this work, the consequences on this specifie set of genes of the whole-genome duplications that occurred during vertebrate evolution were investigated. Whereas most genes a re lost after a w hole- genome duplication event, this work shows that pigmentation genes and other genes within their families have been more retained compared to the average observed genome retention. This was particularly the case for the teleost-specific whole-genome duplications . Hence, this high retention rate could  be related to the high pigmentation diversity observed in the teleost fish lineage, both  in terms of patterns and of pigment cell types . In addition, during this PhD thesis, pigmentation in an emerging model organism, the clownfish Amphiprion ocellaris, was investigated. The white color in clownfish was shawn to be due to specifie pigment cells,  iridophores, and new iridophore genetic markers were detected . One such marker is almost exclusively restricted to ray-finned fish and could have been acquired through a horizontal gene transfer event that occurred at the onset of the evolution of this lineage. Last, in this work, the genetic basis of pigmentation acquisition was scrutinized during the development of clownfish A. ocellar is, and especially during metamorphosis - a major life history transition  in coral  reef  fish . In particular, the  deployment  during  development  of thyroid  hormone signaling  which is a key pathway in metamorphosis regulation in vertebrates  was examined.