Reconstruction of historical relationships between geographic regions within a species’ range, determined through phylogeographic study, can indicate dispersal patterns and help predict future responses to shifts in climate. Ascaphus truei (coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques — microsatellite and genotype-by-sequencing (GBS) — to compare the within region genetic diversity of populations near the northern extent of the species’ range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving towards the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean observed heterozygosities for both techniques (microsatellite, M = 0.19, SE = 0.073; GBS, M = 0.028, SE = 0.0011) and the southernmost region had the highest (microsatellite, M = 0.86, SE = 0.072; GBS, M = 0.18, SE = 0.0027). For both genetic techniques, geographic regions (N=5) separated into 4 genetic clusters with the two most northern regions clustering together. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of A. truei to climate change.