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The true biodiversity of Australia's alpine and subalpine endemics is unknown. Genetic studies to date have focused on sub-regions and restricted taxa, but even so, indicate deep divergences across small geographic scales and therefore that the bulk of biodiversity remains to be discovered. We aimed to study the phylogeography of the Australian Alps by focusing on the skyhoppers (Kosciuscola), a genus of five species of flightless grasshoppers whose combined distributions both span the region and are almost exclusively contained within it. Our sampling covered 650 km on the mainland and several sites in Tasmania with total of 260 specimens used to reconstruct a robust phylogeny of Koscisucola. Phylogenies were based on single nucleotide polymorphism data generated from double-digested restriction-associated DNA sequencing. Skyhoppers diverged around 2 million years ago and have since undergone complex diversification seemingly driven by climatic oscillations throughout the Pleistocene. We recovered not 5 but 14 clades indicating the presence of many unknown species. Our results support conspicuous geographic features as genetic breaks; e.g. the Murray Valley, and inconspicuous ones; e.g. between the Bogong High Plains and Mt Hotham. Climate change is progressing quickly in the region and its impact, particularly on snow, could have severe consequences for the skyhoppers' overwinter survival. The true diversity of skyhoppers highlights that biodiversity loss in the Alps as a result of climate change is likely to be far greater than what can be estimated based on current species numbers and that management including small geographical scales is key. [ABSTRACT FROM AUTHOR]