The mammalian skull base ossifies from chondral elements into successive bones described as the basicranial stem or axis. The axes included the basioccipital, basisphenoid, presphenoid, and mesethmoid bones. Tracing the accurate ontogenetic origin of this area is essential, as endochondral development plays a crucial role in understanding the homology of these axial bones. It contributes to building the ethmo-sphenoidal area and is reflected in the phylogeny. In our study, we examined the ontogeny of the neurocranial base and allied bones (i.e., alisphenoids and orbitosphenoids) in representatives of two living armadillo clades: Dasypus hybridus (n = 18) (Dasypodidae), Chaetophractus vellerosus (n = 9) and Chaetophractus villosus (n = 11) (Chlamyphoridae). The presphenoid is not ossified in Dasypus hybridus, Chaetophractus villosus, or C. vellerosus; moreover, there is no clear evidence that this bone ossifies in other cingulates. In addition, our evidence supports the existence of postnatal mesethmoid ossification in armadillos; reinforces the idea of a different ontogenetic trajectory in armadillos, precocial for Dasypus and altricial for Chaetophractus; and proposes that the presence of the mesethmoid is a primitive character for Eutheria.