Several attempts to include post-Devonian lungfish in phylogenies of dipnoans have been made, but are hampered by the poor preservation of most Mesozoic and Cenozoic lungfish, and by the paucity of the occurrences of these taxa. This contribution has made use of the few post-Devonian fossils that are known from cranial, dental and post-cranial remains, to compare them with Devonian material and with living lungfish. Characters have been chosen to cover the best preserved structures of the Mesozoic and Cenozoic fossils, and the resulting phylogeny has been discussed in relation to previous analyses. The post-Devonian phylogeny has been anchored to a published phylogeny of Devonian taxa and a phylogenetic diversity curve has been computed. Based on this phylogeny rates of origination and extinction have been calculated, and environmental transfers and trends in body size changes have been detected. Our analyses show that the Permian gnathorhizodontids and the extant lepidosirenids are closely related, that lungfishes have experienced two phases of taxic diversification, a marine one in the Devonian and a freshwater one in the Permian. Major negative size shifts occurred during the marine phase and major positive size shifts occurred during the freshwater phase. A new classification of post-Devonian dipnoan families is also presented.