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Anthropogenic climate change is causing a world‐wide reduction of alpine habitat, leaving many high‐elevation species restricted to sky‐islands and vulnerable to extinction. Understanding the genetic parameters of these populations provides key insight into species diversity, dispersal capacity and vulnerability to disturbance. We examined the impact of past climatic variation on a threatened alpine endemic lizard, the Guthega skink, Liopholis guthega. We analysed SNP and mtDNA data to determine the population structure and phylogeny within this species, providing an understanding of the species’ relatedness, dispersal and viability. We identified significant genetic structure, with the split between populations in Koscuiszko National Park, New South Wales (NSW) and the Bogong High Plains, Victoria (VIC) consistent with Plio‐Pleistocene divergence. However, we also detected evidence of possible historical …