The ant-tended Australian butterfly, Jalmenus evagoras, has been a model system for studying the ecology and evolution of mutualism. A phylogeographic analysis of mitochondrial DNA cytochrome oxidase I sequences from 242 butterflies (615 bp) and 66 attendant ants (585 bp) from 22 populations was carried out to explore the relationship between ant association and butterfly population structure. This analysis revealed 12 closely related butterfly haplotypes in three distinct clades roughly corresponding to three allopatric subpopulations of the butterflies. Minimal genetic diversity and widespread haplotypes within biogeographical regions suggest high levels of matrilineal gene flow. Attendant ants are significantly more diverse than was previously thought, with at least seven well-defined clades corresponding to independent morphological determinations, distributed throughout the range of the butterflies. Nested analysis of molecular variance showed that biogeography, host plant, and ant associate all contribute significantly in explaining variation in butterfly genetic diversity, but these variables are not independent of one another. Major influences appear to come from fragmentation due to large-scale biogeographical barriers, and diversification following a shift in habitat preference. A consequence of such a shift could be codiversification of the butterfly with habitat-adapted ants, resulting in apparent phylogenetic concordance between butterflies and ants. The implications of these results are discussed in terms of possible effects of ant attendance on the diversification of Lycaenidae as a whole.