Colors and their patterns are fascinating phenotypes with great importance for fitness under natural conditions. For this reason and because pigmentation is associated with diseases, much research was devoted to study the genetics of pigmentation in animals. Considerable contribution to our understanding of color phenotypes was made by studies in domesticated animals that exhibit dazzling variation in color traits. Koi strains, the ornamental variants of the common carp, are a striking example for color variability that was selected by man during a very short period on an evolutionary timescale. Among several pigmentation genes, genetic variation in Melanocrtin receptor 1 was repeatedly associated with dark pigmentation phenotypes in numerous animals. In this study, we cloned Melanocrtin receptor 1 from the common carp. We found that alleles of the gene were not associated with the development of black color in Koi. However, the mRNA expression levels of the gene were higher during dark pigmentation development in larvae and in dark pigmented tissues of adult fish, suggesting that variation in the regulation of the gene is associated with black color in Koi. These regulatory differences are reflected in both the timing of the dark-pigmentation development and the different mode of inheritance of the two black patterns associated with them. Identifying the genetic basis of color and color patterns in Koi will promote the production of this valuable ornamental fish. Furthermore, given the rich variety of colors and patterns, Koi serves as a good model to unravel pigmentation genes and their phenotypic effects and by that to improve our understanding of the genetic basis of colors also in natural populations.