The origins of the vertebrates have been a topic of debate for several centuries. Much of what we understand about the origins of our own complex body plan has been based on comparative morphological studies between the body plan of vertebrates and the simpler, basal chordate lineages. Amphioxus, one of these simple chordates, is broadly considered to best represent the early origins of our own phylum. Recently, developmental biology has given additional molecular tools to further investigate vertebrate origins. The conclusions from these studies have largely confirmed those reached from comparative morphology, and cemented amphioxus as the only informative outgroup for understanding vertebrate evolution. Our work adds a new perspective to the origins of vertebrates. Hemichordates are a phylum closely related to chordates, but with a divergent body plan organization. Despite this organizational and morphological disparity, our detailed studies during hemichordate early development reveal that hemichordate and vertebrate basic axial patterning share exquisite similarities. Some of these similarities are not shared between amphioxus and vertebrates despite their much closer morphological affinities. I will discuss the implications of our findings for early vertebrate origins, but also what our data suggests about the rather loose connection between gene regulatory network evolution and morphological innovation.