Of the many unique chronicles of development and paleontology, none are so compelling as the transition from fins to limbs. What causes effected the development of our ancestors in the transition from an exclusively aquatic to primarily terrestrial lifestyle? Researchers have sought to answer this question by probing the developmental and genetic processes that build both fins and limbs, revealing extensive parallels in the networks which pattern these structures. This thesis is a contribution to that body of knowledge through my exploration of common developmental programs in paired and median fins as well as shared regulatory features of limb and fin patterning. In Chapter I, I discuss the challenge of assessing homology at various levels, introduce hypotheses on the origin of paired appendages, and overview the shared gene networks between fins and limbs. In Chapter II, I characterize gene expression in paddlefish and skate fins and submit that a common developmental module featuring 5’ Hox genes is present in both paired and median fins. In analyzing the phenotype of hoxa13 zebrafish (Danio rerio) mutants, I found that dorsal and pectoral fin dermal elements were severely truncated, indicating that hoxa13 is necessary for proper dorsal and pectoral fin development. This work lends experimental support to the hypothesis that this developmental module originated in the midline and was later co-opted in development of paired fins. In Chapter III, I used mouse and zebrafish transgenics to assess the functional conservation of the ZRS, a limb-specific Sonic hedgehog (Shh) enhancer, from multiple donor organisms and conclude that this element likely originated in the ancestor of gnathostomes. I also analyzed the pectoral fin phenotype of a ZRS medaka mutant with a reduced number of proximal radials. This result suggests a role for Shh in specifying the number of endoskeletal elements in fins. I end in Chapter IV by proposing that future avenues of research must fully characterize the developmental regulatory networks that define the identity of a body part, providing insight on both the evolutionary origin of such parts and the deep homology of networks. I argue that from using modern genetic and epigenomic techniques to characterize these networks, there will emerge broader commonalities in the evolution of generative processes. Two appendices accompany this dissertation.