Four complete isolated neurocrania excavated during the nineteenth century in the Autun Basin (Sa^one-et-Loire, France) were used by Heyler & Poplin (1982) to erect two species: the symmoriiform Bibractopiscis niger and the xenacanthiform Orthacanthus commailli. However, the specimens have not been mechanically prepared and only a portion of their anatomy is available, complicating their systematic attribution. We revise their systematic status by using X-ray computed microtomography and new comparative material from the Bourbon l’Archambault Basin (Allier, France). This method allows access to the hidden anatomy of the specimens and new systematic revision: we propose O. commailli to be left in open nomenclature as ?Xenacanthimorpha. The specimens attributed to B. niger encompass two distinct morphologies: the holotype, one paratype and a neurocranium from the Bourbon l’Archambault Basin are identified as cf. Triodus sp. The last paratype is left in open nomenclature as ‘Ctenacanthiformes’ indet. We included these neurocrania in geometric morphometric and cladistic analyses of a large sample of Palaeozoic chondrichthyans. Based on the results we propose an evolutionary scenario for the neurocranial transition between the orders ‘Ctenacanthiformes’ and Xenacanthiformes. This transition mostly affects the ethmo-orbital region. The revision of the diversity of these chondrichthyan faunas calls into question potential differences in trophic structures between the different European Carboniferous–Permian basins.