This study investigated spatial genetic structuring of two groups of Australian Ogyris butterflies (Lycaenidae). Ogyris represents one of several Australian endemic butterfly radiations that is well characterised in terms of basic biology but lacking in data useful for discriminating among the potential factors promoting divergence and speciation. A phylogeographic approach was used to document structuring in mitochondrial DNA markers (mtDNA) across the geographic range of two groups of closely related taxa. These include a pair of sister species: Ogyris zosine and O. genoveva, and the polytypic species O. amaryllis which is comprised of four subspecies. Topological relationships among recognised taxonomic units were tested and polyphyletic patterns investigated as a potential source of information relating to divergence and speciation. Sister species Ogyris zosine and O. genoveva were found to exhibit a polyphyletic relationship based on mtDNA. The deepest divergence within the group separated allopatric populations of O. zosine in northern Australia which do not correspond to a recognised taxonomic entity. The distribution of O. zosine and O. genoveva is parapatric along the east coast and additional sampling in this area along with evidence from allozyme markers revealed that the polyphyletic pattern can be explained by past mtDNA introgression at the current contact zone. The two species engage in an obligate mutualistic association with different suites of Camponotus ant species. It is hypothesised that this association may be involved in maintaining differentiation between the taxa through ant-mediated selection against hybrids. The distribution of a blue/purple wing colour polymorphism in female O. zosine is consistent with the role of wing colour as a prezygotic isolating mechanism in the contact zone although other explanations cannot be excluded. Genetic relationships were examined among four nominal taxa of the polytypic species Ogyris amaryllis which have a combined distribution spanning most of mainland Australia. Mitochondrial sequence data recovered a putatively ancestral and polyphyletic inland subspecies with several peripheral subspecies showing reduced variation within this topology. Analysis of spatiotemporal patterns of variation for the inland subspecies indicated a recurrent history of restricted gene flow and range expansion through the Pleistocene, while peripheral subspecies are characterised by higher levels of population structure and a history of population fragmentation. High levels of variation and population differentiation observed for allozyme markers were not consistent with subspecies boundaries. Partitioning of allozyme variation was explained better by arranging populations according to their larval host plant. Genetic data, combined with information on distribution and ecology, are consistent with a pattern of peripheral isolation associated with host plant specialisation of coastal populations in the O. amaryllis complex.