Climate change will cause relict alpine glaciers to disappear within decades. Associated high-altitude streams will face significant hydrological changes that might affect population genetic diversity of lotic species. In a recent study of glacier-fed streams in the Pyrenees, Finn et al. (2013) predicted that a large proportion of regional genetic diversity of the mayfly Baetis alpinus would be lost as glacial meltwater sources disappear. We expanded the analysis of Finn et al. to include genetic data (mitochondrial barcoding region) collected from B. alpinus occupying recently deglaciated locations including multiple basins in 2 mountain ranges (Sierra Nevada and Picos de Europa) on the Iberian Peninsula and 1 additional, deglaciated Pyrenean basin. We hypothesized that regional genetic diversity at scales of entire mountain ranges (γ diversity) and population structure within ranges (β diversity) would be lower in recently deglaciated mountain ranges than in the still-glaciated Pyrenees. For 4 cryptic lineages of the B. alpinus species complex in 3 mountain ranges, we found significantly lower genetic diversity in recently deglaciated than glaciated regions. β and γ genetic diversity were correlated, suggesting that population structure (β) strongly influences total regional diversity. Results support the hypothesis of Finn et al. (2013) that disappearance of alpine glaciers will result in substantial loss of genetic diversity. The distinctive hydrological environment created by glacial meltwater might drive an interaction between reproductive barriers (between highly and minimally glacier-influenced reaches within basins) and physical barriers (isolating highly glacier-influenced reaches among basins) that amplifies regional genetic diversity in mountain ranges still containing alpine glaciers.