Butterfly wing color patterns result from the arrangement of monochromatic scales containing chemical pigments and a delicate architecture that can cause interference or diffraction of light, generating iridescent colors. The latter mechanism is known as structural coloration and, despite its ecological importance, little is known about the molecular mechanisms underlying the development of this trait. The Southern Dogface butterfly, Zerene cesonia, exhibits sexually dimorphic development of ultraviolet wing reflectance. Males possess a UV-reflective patch on the forewing that results from nano-structures on the wing scales, which are absent in females. This dimorphism offers an excellent opportunity to explore the genetic mechanisms involved in pattern formation and cyto-structural variation. We used RNA-seq data from imaginal wing discs through late larval and pupal development to identify genes involved in the regulation of color pattern and scale structure formation. We identified candidate genes for the regulation of wing color pre-patterning and sexually-dimorphic development of wing scales. Our results provide a genomic resource for the identification and characterization of genes that participate in the regulation of wing development in pierid butterflies.