AbstractHere, we define a research program using primordial skull characters for broad scale phylogenetic comparisons, particularly for amniotes. There are many chondrocranium descriptions in the literature, encompassing many clades of vertebrates. The definition of a comparable “tempus optimum” for fully formed chondrocrania, as developed herein, will enable discrete character definition in the sense of phylogenetic systematics. The “tempus optimum” is a time period in which the nose region shows full chondrification and the basicranium has not yet changed in its anatomy by ossification processes. For studies on heterochrony, changes in the developmental timing through evolution, the available data in the literature are insufficient. Anatomical standardizations, traceable methodological approaches and clear definitions of comparable developmental stages are needed. Moreover, for profound homology assertions of chondrocranial structures, ontogeny needs to be traced from early mesenchymal condensation, through several stages of cartilage development, up to postnatal stages, in which ossifications are already present. A holistic observation, including hard and soft tissue anatomy, is of paramount importance to generate hypotheses of homology with much explanatory power and to derive conclusions on functional morphology. For that, traditional histological methodology is needed. We exemplify the suggested approach in two case studies on the disputed laterosphenoid in turtles and crocodiles and on the homology of pila antotica in a pleurodire turtle, and, using here defined criteria, we formulate hypotheses on their homology.