The phylogenetic history of rudist bivalves is reviewed using a cladistic analysis based on 41 morphological shell characters and a new topology is proposed. A novel approach to rudist comparative anatomy has enabled the mapping of homologous zones. We highlight that ‘pallial canals’ can be homologous to four specific cavities that have merged during rudist evolution. The characters of the myophores and muscle insertions have also been reappraised using a hierarchical scheme. We formalize, for the first time, the complex diversification of rudist myophores by constructing tree-like characters that can contain up to six informative states for each of the four myophores. All characters have been coded as independent features. This has enabled the identification of different evolutionary rates of change between left and right valves and allows the recognition of the various morphoanatomic responses of one valve to the structural changes of the other. All characters have been coded in hierarchies and analysed in three-taxon analysis. Taxonomic sampling composed of two species per family allows an exhaustive monophyly test of all families of the suborder Hippuritidina. Only the families Polyconitidae, Plagioptychidae, Radiolitidae and Hippuritidae are found to be monophyletic. The two superfamilies are both found to be polyphyletic. The Hippuritidae is found to be the sister group of the Radiolitidae. Pachytraga is found as the sister group of all the rudists with pallial canals except Sellaea. Two evolutionary radiations in rudists are dated, using the cladistic concept of temporal hierarchy, to the Hauterivian + and the Albian+.