The evolution of wings and the adaptive advantage they provide have allowed insects to become one of the most evolutionarily successful groups on earth. The incredible diversity of their shape, size, and color patterns is a direct reflection of the important role wings have played in the radiation of insects. In this review, we highlight recent studies on both butterflies and Drosophila that have begun to uncover the types of genetic variations and developmental mechanisms that control diversity in wing color patterns. In butterflies, these analyses are now possible because of the recent development of a suite of genomic and functional tools, such as detailed linkage maps and transgenesis. In one such study, extensive linkage mapping in Heliconius butterflies has shown that surprisingly few, and potentially homologous, loci are responsible for several major pattern variations on the wings of these butterflies. Parallel work on a clade of Drosophila has uncovered how cis-regulatory changes of the same gene correlate with the repeated gain and loss of pigmented wing spots. Collectively, our understanding of formation and evolution of color pattern in insect wings is rapidly advancing because of these recent breakthroughs in several different fields.