Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or secondarily lost their shell. Monoplacophora were not included in molecular studies until recently, when it was proposed that they constitute a clade with chitons named Serialia, reflecting the serial repetition of body organs in both groups. Attempts to understand the early evolution of molluscs become even more complex when considering the large diversity of Cambrian fossils. These can have multiple dorsal shell plates and sclerites, or be shell-less but with a typical molluscan radula and serially repeated gills. In order to better resolve the relationships among molluscs we generated transcriptome data for 15 molluscs that, in combination with existing data, represent for the first time all major molluscan groups. We analysed multiple data sets containing up to 216,402 sites and 1185 gene regions using multiple models and methods. Our results support a clade Aculifera, containing the three molluscan groups with spicules but without true shells, as well as the monophyly of Conchifera—the shelled molluscs. Monoplacophora are not the sister group to other Conchifera, but constitute the sister group to the highly modified cephalopods. Strong support is found for a clade comprised of Scaphopoda (tusk shells), Gastropoda, and Bivalvia, with most analyses placing Scaphopoda and Gastropoda as sister groups. This well-resolved tree will constitute a framework for further studies in mollusc evolution, development and anatomy.