Conodonts represent the earliest vertebrate group to have developed extensively mineralized tissues, providing a unique record of the early evolution of vertebrate biomineralization. Herein, we investigate the crystallographic differences between paraconodonts and euconodonts through an integrated characterization of their bioapatite structure. A broad dataset of conodont elements ranging from the Cambrian to the Triassic was investigated by electron microscopy and X-ray microdiffraction, with particular emphasis on bioapatite unit-cell parameters, Crystallinity Index (CI) and number of coherently diffracting unit-cell repeats. Taken together, the investigated parameters reveal distinct crystallographic distributions for paraconodonts and euconodonts. Paraconodonts occupy a comparatively restricted crystallographic field, characterized by lower a and higher c unit-cell parameters, smaller unit-cell volumes, lower CI values, and smaller crystallite dimensions, whereas euconodonts show generally higher crystallinity and substantially greater crystallographic variability. Although carbonate content was not measured directly, the unit-cell differences are consistent with higher carbonate content in paraconodont bioapatite. Differences in crystallite development along the a and c axes further suggest that the transition to the euconodonts did not involve a simple increase in crystallinity or isotropic crystal growth, but rather a reorganization of apatite at the crystallographic scale. No clear differences were detected between basal and denticle regions in selected euconodonts, and CI showed no clear association with the conodont Color Alteration Index (CAI). The group-level crystal-chemical differences may retain a biological component, although unequal sample sizes, taxonomic composition, and diagenetic variability limit its isolation. Remarkably, the mineralogical differences identified herein between paraconodont and euconodont bioapatite parallel those distinguishing dentine and enamel/enameloid in more advanced vertebrates. More specifically, qualitative comparison with differentiated dental tissues of fossil and extant catsharks reveals partial correspondence between paraconodonts and shark roots and between euconodonts and shark crowns, although these similarities do not imply tissue homology. This correspondence suggests that the transition from paraconodont to euconodont mineralization may have captured an early stage in the differentiation and specialization of vertebrate mineralized tissues, potentially providing insight into the emergence of distinct tissue types during the early evolution of the vertebrate skeleton.

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