Phylogeographic structure is a product of a species' life history and dispersal patterns, geographic history, climatic history and chance. Comparative phylogeography, using carefully chosen model species, can highlight the relative contribution of each of these factors and identify common processes affecting communities. In this study we compare and contrast fine-scale phylogeographic patterns in two ground-dwelling species of water skink, Eulamprus heatwolei and Eulamprus tympanum, from the biogeographically well-characterized Tallaganda region in south-eastern Australia, and compare them against data from a number of invertebrate species from the same region. Using variation in mitochondrial sequence, we have uncovered dramatically different biogeographic histories for the two species, despite their marked behavioural and morphological similarity. Eulamprus tympanum shows an average corrected sequence divergence of 0.014 and patterns of geographic variation in haplotypes consistent with historical vegetational changes resulting from past glaciation cycles. In contrast, E. heatwolei shows an average divergence of only 0.0075, and geographic structure that reflects a recent and rapid colonization, perhaps following an ice age local extinction. These two contrasting patterns of variation have also been identified in invertebrate taxa as disparate as collembolans and spiders; these species show either deep structure, associated with local persistence, or little variation of structure, which we attribute to recent extinction and re-colonization. We argue that historical persistence versus extinction is a consequence of (often minor) differences in lifestyle and local habitat preference.