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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 …