The Palaeoheterodonta is a diverse clade consisting of the freshwater bivalve order Unionoida and its marine sister group, Neotrigonia. Neotrigonia is the sole surviving genus of the Trigonioida, known from only six species in Australian waters. Unionoids (freshwater mussels), in contrast, are widespread on all continents except Antarctica and are represented by c. 900 species. Discussion is biased towards the freshwater mussel condition, but Neotrigonia is crucial as a ‘living fossil’ for establishing the plesiomorphic states of unionoid synapomorphies. Neotrigonia retains many of the characters of the ancestral heteroconch. Our object is to provide evidential support for the natural classification of the extant Palaeoheterodonta. A supermatrix of 50 taxa and 1183 characters was constructed from 62 previously published DNA sequences of mitochondrial cytochrome oxidase subunit I (COI) and 28S nuclear ribosomal DNA, 15 novel sequences, and 59 morphological characters. Published COI sequences for Coelatura aegyptiaca, Pseudomulleria dalyi, and Obliquaria reflexa were treated as potentially problematic because of their inconsistency under different methodological assumptions and conflict with other datasets. Each partition was analysed under the criterion of parsimony separately and in combined analyses; analyses were run both with and without the problematic sequences. From our ‘combined evidence’ topology (with problematic sequences excluded), the Unionoida is monophyletic on the basis of eight synapomorphies, including larval parasitism, brood protection, and restriction to freshwater. The order is composed of six families in two superfamilies, Unionoidea and Etherioidea: ((Unionidae + Margaritiferidae) + (Hyriidae + (Etheriidae + (Mycetopodidae + Iridinidae)))). The morphological synapomorphies of these taxa are discussed with an emphasis on both the diagnosing of taxa and highlighting areas of ambiguity and missing data. Three appendices provide descriptions of the morphological characters (Appendix 1), a diagnosis of apomorphies for all branches of the phylogeny (Appendix 2), and a family-level classification of the extant Palaeoheterodonta, including a complete synonymy (Appendix 3). © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 148, 343–394.