The allopatric model of biological speciation involves fracturing of a pre-existing species distribution and subsequent genetic divergence in isolation. Accumulating global evidence from the Pyrénées, Andes, Himalaya, and the Southern Alps in New Zealand shows the Pleistocene to be associated with the generation of new alpine lineages. By synthesising a large number of genetic analyses and incorporating tectonic, climatic, and population-genetic models, we show here how glaciation is the likely driver of speciation transverse to the Southern Alps. New calibrations for rates of molecular evolution and tectonic uplift both suggest a ⿼2 million-year (Ma) time frame. Although glaciation is often seen as destructive for biodiversity, here we demonstrate its creativity, and suggest a general model for speciation on temperate mountain systems worldwide.