We conduct a phylogeographic and population genetic study of the Asiatic Toad (Bufo gargarizans) to understand its evolutionary history, and the influence of geology and climate of the region. A total of 292 individuals from 94 locations were genotyped for two mitochondrial DNA loci (cytb, ND2 gene) and five nuclear introns (Sox9-2, Rho-3, CCNB2-3, UCH-2, DBI-2). We performed a suite of phylogenetic, population genetic, and divergence dating analyses. The phylogenetic trees constructed using mitochondrial loci inferred B. gargarizans being divided into two major groups: West (China mainland) and Northeast (Northeast China, Russia and Korean Peninsula). As with previous studies of this species, we recover population genetic structure not tied to geographic region. Additionally, we discover a new genetic clade restricted to Northeast Asia that points towards the Korean Peninsula being a glacial refugium during the Pleistocene. The weak phylogeographic pattern of B. gargarizans is likely the result of multiple biological, anthropogenic, and historical—robust dispersal abilities as a consequence of physiological adaptations, human translocation, geologic activity, and glacial cycles of the Pleistocene. We highlight the complex geologic and climatic history of Northeast Asia and encourage further research to understand its impact on the biodiversity in the region.