The questions of how features such as shape and size are regulated at the cellular level and encoded in the genome are a mainstay in evolutionary and developmental biology. Complex traits like shape are quantitative and polygenic in nature. Of all possible complex and quantitative traits, the head is perhaps the most intricate morphological feature. It is the major structure through which bilateral animals perceive and interact with their environments, and is thus a crucible for interactions between form, function, evolution and development. This complexity is reflected in the gene networks underlying head development, and the complex genetic interactions that participate in head development. Historically, epistasis has been quite difficult to study due to complications of dominance effects and extremely rapid increase in the number of progeny required to detect gene interactions. Haploid systems, however, provide greater power in detecting recessive epistatic interactions than diploid systems, due to exposure. The genus Nasonia of parasitoid wasps is particularly suited for epistatic studies of craniofacial morphogenesis due to their haplodiploid genetics, sex-specific morphologies in head shape, and ability of interspecies crosses. Furthermore, F2 hybrid males display considerable variation and abnormalities in craniofacial phenotypes, which contributes to the mapping of quantitative trait loci involved in development and morphology. In this thesis we examine the varying forms of facial anomalies in hybrid male wasps and delve deeper into the gene interactions that affect development and morphogenesis in male heads. Additionally, we observe the physical development of Nasonia’s imaginal discs to establish a definitive timeline of larval development in Nasonia. In addition to the genetic and morphometric findings within these experiments, a number of novel tools and methods were developed. Together, these results broaden the possibilities of using Nasonia to study the field of evolutionary developmental genetics.