The history of life is marked by near constant morphological transformations, preserved in part by the fossil record. Unfortunately, the developmental mechanisms that drove many key morphological transformations are not well understood. In order to study these morphological transformations and their underlying developmental mechanisms, an integrative approach synthesizing data from palaeontological, phylogenetic, and developmental sources is required. Here, I have focused on improving our understanding of one such transformation, the morphology and development of the skull-neck boundary in lissamphibians. To complete this goal, I tested two hypotheses. First, that the skull-neck boundary and composition of the occiput observed in extant lissamphibians is the result of a secondary reduction compared to their fossil relatives. Second, that changes in Hox gene expression domains can cause homeotic transformations of skull-neck boundary structures in two lissamphibian model organisms, Ambystoma mexicanum (salamanders) and Xenopus laevis (frogs). I found using phylogenetic analyses and ancestral state reconstructions that the lissamphibian occipital morphology is secondarily derived when compared to their fossil relatives. Then, I described the development of the skull, focusing on the occiput, in A. mexicanum and X. laevis using cell-lineage tracing techniques to track somitic contributions to the skull, hypoglossal nerve complex morphological data, and traditional whole-mount cartilage and bone staining techniques. Finally, I perturbed Hox gene expression patterns to produce homeotic transformations via exogenous retinoic acid and a retinoic acid inhibitor (citral) and described the resulting skull morphology. I provided evidence that homeotic transformations of skull-neck boundary structures could be induced via changing retinoic acid concentration in the developing embryo: first with the position of the hypoglossal nerve complex relative to skeletal structures along the anterior-posterior axis and second with GFP-labelled somite cell-lineage tracing. The resulting morphologies indicate that it is likely that changing Hox gene expression domains resulted in the unique lissamphibian morphology at the occiput and the derived position of their skull-neck boundary. This research contributes to our understanding of the evolution of the unique lissamphibian skull-neck morphology. My integrative approach has helped to elucidate the relationship between morphological transformations and the developmental processes underlying them.