The Middle Ordovician to Late Silurian represents an interval of approximately 50 million years, which has been recognised as the initial, cryptic, period in the evolutionary history of chondrichthyan fish. The fossil remains attributed to early chondrichthyans are dominated by isolated dermal scales that predate the appearance of undisputed chondrichthyan teeth and articulated skeletons in the Lower Devonian. Investigation of the inter-relationships of these scale taxa and their systematic position relative to high- ranked chondrichthyan clades has been hampered by the lack of developed scale-based classification schemes for jawed gnathostomes, coupled with the limited use of scale characters in phylogenetic studies of Palaeozoic Chondrichthyes. Here, all previously documented scale types of alleged Lower Palaeozoic chondrichthyans were examined using a combination of X-ray microtomography, SEM and Nomarski DIC optics. These were found to exhibit a set of characteristics (symmetrical trunk scales, areal crown growth and lack of hard-tissue resorption, cancellous bone and enamel) recognised as specific to the dermal skeleton of chondrichthyans among derived gnathostomes. The collected data permitted the establishment of a hierarchy of scale characters for separate taxonomic ranks, leading to the recognition of three Orders (Mongolepidida, Elegestolepida ordo nov. and Altholepida ordo nov.) of early chondrichthyans, differentiated by distinct types of scale-crown morphogenesis. A scale-based cladistic analysis of jawed gnathostomes corroborated these results by recovering a chondrichthyan clade that incorporates all examined taxa and ‘acanthodians’ with non-superpositional crown growth patterns. It is thus proposed that chondrichthyan dermoskeletal characters carry a phylogenetic signal, allowing to interpret the documented diverse types of scale morphogenesis as evidence for a major radiation of chondrichthyan lineages in the Lower Palaeozoic.