There is a growing appreciation of impacts of late-Quaternary climate fluctuations on spatial patterns of species and genetic diversity. A major challenge is to understand how and why species respond individualistically to a common history of climate-induced habitat fluctuation. Here, we combine modelling of palaeo-distributions and mitochondrial-DNA phylogeographies to compare spatial patterns of population persistence and isolation across three species of rainforest skinks (Saproscincus spp.) with varying climatic preferences. Using Akaike Information Criterion model-averaged projections, all three species are predicted to have maintained one or more small populations in the northern Wet Tropics, multiple or larger populations in the central region, and few if any in the south. For the high-elevation species, Saproscincus czechurai, the warm–wet climate of the mid Holocene was most restrictive, whereas for the generalist S. basiliscus and lower-elevation S. tetradactyla, the cool–dry last glacial maximum was most restrictive. As expected, S. czechurai was the most genetically structured species, although relative to modelled distributions, S. basiliscus had surprisingly deep phylogeographical structure among southern rainforest isolates, implying long-term isolation and persistence. For both S. basiliscus and S. tetradactyla, there was high genetic diversity and complex phylogeographical patterns in the central Wet Tropics, reflecting persistence of large, structured populations. A previously identified vicariant barrier separating northern and central regions is supported, and results from these species also emphasize a historical persistence of populations south of another biogeographical break, the Tully Gorge. Overall, the results support the contention that in a topographically heterogeneous landscape, species with broader climatic niches may maintain higher and more structured genetic diversity due to persistence through varying climates.