The typical pattern of morphological evolution associated with the radiation of a group of related species is the emergence of a novel trait and its subsequent diversification. From butterfly eyespots and their various colorful rings to the diversity of shapes assumed by vertebrate teeth, seashells or horn beetles, this pattern of emergence-diversification holds for countless characters across most animal groups. Yet, the genetic mechanisms associated with these two evolutionary steps are poorly characterised. We have characterized some of the genetic changes underlying the evolution and the diversification of a wing pigmentation pattern in some Drosophila species. Our results show how a primitive spot of dark pigment on fly wings has first evolved from the assembly of a novel gene regulatory module whereby pigmentation genes fell under the regulation of a common transcriptional activator. The primitive wing spot pattern subsequently diversified through the sole changes in spatial distribution of this activator. These results suggest that the genetic changes underlying the emergence and the diversification of the wing pigmentation patterns are partitioned within genetic networks. More generally, this two-step model accounts at the gene regulatory level for the general pattern observed in animals and plants where morphological diversification mostly results from occasional novelties and infinite variations on these new themes.