Mitochondrial DNA sequences consisting of 645 sites from the 12S rRNA and 16S rRNA genes were used to estimate the phylogeny of 15 of the 32 species of spiny-footed lizards Acanthodactylus. The resultant tree has similarities to that produced from a differentially weighted data set of 32 morphological characters but there are also significant differences. However, combined analysis of molecular and morphological data sets produces the same tree topology as DNA sequence alone. The molecular data confirm that there are distinct eastern and western clades within Acanthodactylus, but place A. boskianus in the former while the A. scutellatus group constitutes a third clade. Species for which only morphological information is available were integrated with the combined tree to give a provisional phylogeny for 31 species. This phylogeny indicates that the ancestor of existing Acanthodactylus probably originated in south-west Asia and that North Africa was invaded by more than one lineage of the genus. It also suggests that soft aeolian sand habitats may have been independently occupied more than once. Molecular data provide independent evidence that the differential weighting of morphological characters in past analyses was appropriate.