Allopatric divergence drives the genetic structuring of an endangered alpine endemic lizard with a sky-island distribution

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 introgressive hybridization between some NSW populations and the VIC populations. Marked within‐site population structure and significant population differentiation among sites within each state were found, indicating a limited dispersal capacity. Higher levels of genetic diversity within NSW support the correlation between elevation and diversity and implicate Kosciuszko National Park as a historic refugia. Low contemporary habitat availability, little to no capacity for elevational progression and low genetic diversity, particularly in VIC, leaves L. guthega highly vulnerable to threatening processes associated with climate change. Conservation management should consider genetic rescue as a potential method to enhance genetic diversity across this species’ range.