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The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal development. To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB) and from dogfish as representative of jawed cartilaginous fish (ScRunx1–3). According to our phylogenetic reconstruction the stem species of chordates harboured a single Runt gene and thereafter Runt locus duplications occurred during early vertebrate evolution. All newly isolated Runt genes were expressed in cartilage according to quantitative PCR. In situ hybridisation confirmed high MgRunxA expression in hard cartilage of hagfish. In dogfish ScRunx2 and ScRunx3 were expressed in embryonal cartilage whereas all three Runt genes were detected in teeth and placoid scales. In cephalochordates (lancelets) Runt, Hedgehog and SoxE were strongly expressed in the gill bars and expression of Runt and Hedgehog was found in endo- as well as ectodermal cells. Furthermore we demonstrate that the lancelet Runt protein binds to Runt binding sites in the lancelet Hedgehog promoter and regulates its activity. Together, these results suggest that Runt and Hedgehog were part of a core gene network for cartilage formation, which was already active in the gill bars of the common ancestor of cephalochordates and vertebrates and diversified after Runt duplications had occurred during vertebrate evolution. The similarities in expression patterns of Runt genes support the view that teeth and placoid scales evolved from a homologous developmental module., Author Summary Important molecular mechanisms underlying mammalian skeletogenesis have been described but knowledge about the evolutionary origin of these gene networks is limited. The Runt gene family (Runx1–3) is of extraordinary importance for skeletogenesis. Runx2 deficient mice completely lack bone. Runx2 and Runx3 are essential for cartilage development and Runx2 regulates the key factor Indian hedgehog, which coordinates skeletogenesis. Here, we reconstructed Runt gene evolution in correlation to skeletal evolution. By analyzing lancelets, one of the closest living relatives of vertebrates, we revealed that the single Runt and Hedgehog family founder genes were co-expressed in primitive skeletal elements of the chordate stem species. Interestingly, at this stage the Runt and Hedgehog pathways were already directly linked to one another. Furthermore we isolated two Runt genes from a representative of jawless cartilaginous fish (hagfish) and three Runt genes from jawed cartilaginous fish (dogfish) which were all expressed in cartilage. The dogfish Runt genes were also found in teeth and placoid scales. This study suggests that Runt genes were involved in all ancient processes of chordate skeletogenesis. Furthermore the analysis supports the theory that most likely the gut was the tissue that originally secreted an acellular gill gut skeleton in the chordate ancestor.