Morphological and genetic aspects of the integumentary system in mouse and chicken are well known, but only few studies investigated those features in reptiles, the basal group of both mammals and birds. In order to contribute to fill this gap, and therefore enlighten amniotes evolutionary relationships, we worked with two non-model species of snakes (i.e., corn snake and puff adder) to furnish exclusive details on the morphogenesis of the complex squamate skin thanks to histological and immunohistochemical analyses. This permitted us to identify previously undescribed structures likely to intervene during early scale development. Quantitative PCR analyses and whole-mount in situ hybridization were performed providing a first overview of the expression pattern of conserved developmental genes well known to regulate epithelial appendage development in other amniotes. We also initiated a comparison between wild-type and scaleless mutant skin in both snakes species in order to give a first overview of morphological differences between those snakes. Such novel project on non-classical model organisms allow to improve our understanding of vertebrate integument Evo-Devo. Moreover epithelial appendages represent a particularly good model to investigate the reutilization of existing signaling pathways in order to create new structures.