Despite advances in our understanding of feather development and avian evolutionary history, little is known about the relationship between feathers and bird scales. To better grasp the relationship between these structures, we examined the genetics of developing feathers and scales in Leghorn chicken embryos. Using transcriptomics, we identified four genes that seemed specific to feathers—Gata3, Ghrh, Akap12, and Tcf7l2. These genes are thought to be involved in the development of the feather sheath, polarization, barb formation, and follicle growth, respectively. Whole-mount in situ hybridizations confirmed the activity of these genes in the feather buds of developing chicken embryos, but not the scales. To further demonstrate the feather specificity of these genes, we also performed whole-mount in situ hybridizations on the legs of Silkie chickens. Silkies are a unique chicken breed with many unusual features, including feathers in areas on the tarsometatarsus and phalanges where scutate scales are normally present. The expression patterns of these four genes on Silkie legs matched patterns observed on the Leghorn chickens. These experiments take advantage of natural morphological variation in chickens to show that the four genes identified by transcriptomics are truly specific to the feather, a morphological structure, rather than a particular location on the body. Thus, these four genes are specific to the development of feathers, but not avian scales.