Aim During the glacial phases, the Andean slopes of southern South America were covered by ice sheets, causing the isolation of many species in glacial refugia. This work aimed to test the number and putative location of glacial refugia in southern South America and establish the sources, timing and direction of post-glacial colonization events. Location Southern South America, Patagonia. Taxon Olive mouse (Abrothrix olivacea). Methods Using exome capture, we genotyped 7339 SNPs in 172 specimens of A. olivacea collected at 21 localities distributed across the steppe, grasslands, and forests in the Patagonian-Fuegian region and seven specimens from two other species of Abrothrix. Based on the effective migration rate, principal component analysis, and admixture composition, we first study the population structure of A. olivacea. The source and direction of colonization events were inferred using the directionality index and standard population genetic analyses. To study the role of the glacial phases, we performed a bayesian demographic analysis to infer divergences times and ancestral population sizes. Results Population genomic analyses based on SNPs of more than 7000 exons identified three Patagonian genetic clusters: Valdivian forests, continental Magellan forests, and a combination of continental open biomes and Tierra del Fuego. The directionality index supports a single source in northwestern forests, in line with a Valdivian forest refugium, from which the post-glacial colonization may have started. The effective diversity rate, the onset of population expansions and divergence times also support a Valdivian forest refugium and rule out a separate southern refugium in Tierra del Fuego. Main conclusions Our results support a coastal refugium located in or near the previously proposed Valdivian refugium and reject in situ differentiation in Tierra del Fuego. More in general, our demographical analysis reveals the role of the Last Glacial Maximum in affecting the population dynamics (i.e., contraction and expansion) of A. olivacea and in fostering the geographical diversification of populations.