Two morphological paradigms have long been used in comparative anatomical studies of bivalves: (1) the primary ligament is three-layered, with the layers corresponding to three shell layers; and (2) the primary mantle edge is composed of three folds with clearly defined functions. The results of studies of larval development indicate, on the contrary, that the primary ligament is completely organic. Calcified, fibrous ligamental material develops from lamellar material near areas of contact between ligament and shell, and development of the fibrous portions then proceeds toward the midline, finally achieving in many lineages a continuous fibrous bridge between valves. Furthermore, these results suggest that the mantle edge in the Bivalvia is primarily twofold and that the only clearly homologous structure between major groups is the periostracal groove itself. These morphological concepts, with other new and previously published data on shell ultrastructure, ligaments, mantle edges, ctenidia, palps, lips, stomachs, muscles, and photoreceptors, lead to a new picture of the evolution of primitive and derived character states in groups previously included in a subclass Pteriomorphia. Furthermore, a cladistic analysis of these data allows predictions of the morphology of ancestors which can be tested by reference to the preserved morphology and sequence of fossils. A new phylogenetic classification separates these groups into three superorders within the subclass Autobranchia: Isofilibranchia (mytiloids), Prionodonta (arcoids), and Pteriomorphia. The most complex radiation has been in the Pteriomorphia. Three orders originated in the early Palaeozoic: Pterioida, Limoida, and Ostreoida. The Pterioida and Ostreoida developed monomyarian, pleurothetic states independently, and each order developed its own mode of shell secretion. Further differentiation in the order Ostreoida occurred in the mid-Palaeozoic, producing two suborders, the Ostreina and Pectinina, both of which had already developed foliated calcitic ultrastructure from simple prismatic structure. By the early Mesozoic, the Ostreina had given rise to three extant superfamilies - the Ostreacea (true oysters), Dimyacea, and Plicatulacea - through atrophy of the foot, the assumption of a pleurothetic state on either the left or right side, and early obligate cementation. The Pectinina, through retention of the foot and the assumption of a pleurothetic mode of life, had evolved before the late Palaeozoic to the Anomiacea and Pectinacea. Within the superfamily Pectinacea, four extant families have origins ranging from early Carboniferous to Cretaceous in age: Propeamussiidae, Pectinidae, Syncyclonemidae, and Spondylidae. The new family Syncyclonemidae, which contains a genus long assumed to have become extinct at the end of the Cretaceous, is here recognized in the Recent and late Pleistocene on opposite sides of the Earth. With regard to extinct groups, many genera previously assigned to the Pteriacean family Malleidae belong in the Ostreacea on the basis of shared derived character states. Incorporation of these taxa as well as the Dimyacea in the Ostreina suggests that oysters have a dimyarian, possibly non-pleurothetic, origin and cannot have evolved from forms like the Pseudomonotids, which retained their foot and became pleurothetic. The new name Buchiacea is introduced for a set of extinct taxa within the suborder Pectinina including the Buchiidae, Monotidae, Oxytomidae, and Pseudomonotidae of previous authors. Derivation of this group is from the common ancestry of the Anomiacea and Pectinacea. The extinct Palaeozoic Aviculopectinidae, Pterinopectinidae, Deltopectinidae, and Leiopectinidae are grouped in a superfamily Aviculopectinacea, which also appears to have branched from the early ancestry of the Pectinina.