This article is an overview of concepts relating to the integration of the genotype and phenotype. One of the major goals of evolutionary developmental biology, or evo-devo, is to understand the transformation of morphology in evolution. This goal can be accomplished by synthesizing the data pertaining to gene regulatory networks and making use of the increasingly comprehensive knowledge of phylogenetic relationships and associated phenotypes. I give several examples of recent success in connecting these different biological levels. These examples help illuminate the “black box” between genotype and phenotype and illustrate a few of the technical and bioinformatic challenges ahead. The key concept of modularity unites genetic, developmental, and evolutionary approaches, because modules are the units of evolution. Primitive and derived network modules interact in development to create the phenotype. To obtain a systems-level understanding of evolutionary phenotypic change, bioinformatics approaches involving ontologies need to be applied, and new methods of visualization need to be developed.