Teeth are a key vertebrate innovation; their evolution is generally associated with the origin of jawed vertebrates. However, tooth-like structures already occur in jawless stem-gnathostomes; heterostracans bear denticles and morphologically distinct tubercles on their oral plates. We analysed the histology of the heterostracan denticles and plates to elucidate their morphogenesis and test their homology to the gnathostome oral skeleton. We identified a general model of growth for heterostracan oral plates that exhibit proximal episodic addition of tubercle rows. The distal hook exhibits truncated lamellae compatible with resorption, but we observe growth layers to be continuous between denticles. The denticles show no evidence of patterns of apposition or replacement indicating tooth homology. The oral plates and dermal skeleton share the same histological layers. The denticles grew in a manner comparable to the oral plate tubercles and the rest of the dermal skeleton. Our test of phylogenetic congruence reveals that the distribution of internal odontodes is discontinuous, indicating that the capacity to form internal odontodes evolved independently several times among stem-gnathostomes. Our results support the 'outside-in' hypothesis and the origin of teeth through the spread of odontogenic competence from extra-oral to oral epithelia and the subsequent co-option to a tooth function in gnathostomes.