Appreciation for the role of ontogeny in plant evolution has been heightened by advances in studying development using molecular techniques, with a growing number of specific structural features now understood in terms of the genetic, regulatory, and biochemical mechanisms by which they are produced. Paleontological approaches to plant development provide a vehicle for extending that understanding to the ontogeny and evolution of whole organisms through time. Recent studies have shown that developmentally diagnostic features can be identified in the fossil record, where they represent fingerprints for gene-mediated regulatory pathways. The first paleontological evidence for the regulation of cambial activity via the polar axial flow of auxin consists of circular patterns of tracheary elements above buds and branch junctions in the wood of the 375-million-year-old fossil progymnosperm Archaeopteris Dawson. That evidence strongly supports homology of secondary vascular tissues in progymnosperms and seed plants, and monophylesis of the lignophytes (progymnosperms and seed plants). Similar anatomical patterns at the same position have now been identified in the wood of tree-sized fossil equisetophytes and arborescent lycophytes that belong to independent lineages, demonstrating that a similar mechanism involving the regulation of secondary vascular tissue production by the polar axial flow of auxin characterizes those clades as well. These data imply that the wood in lignophytes, lycophytes, and equisetophytes originated in conjunction with the parallel evolution of regulation of secondary tissue production by auxin in each clade. The independent origins of secondary vascular tissue in three major clades of Paleozoic plants sensu Kenrick and Crane (1997) reveal evolutionary patterns that are not represented in the living flora and illuminate promising avenues for combining future paleontological studies with molecular and genetic studies to substantially impact our understanding of the role of developmental regulation in vascular plant evolution.