Background <p>The Pacific Northwestern region of North America is inhabited by two distinct subspecies of black-tailed deer, Columbian (<i>Odocoileus hemionus columbianus</i>) and Sitka (<i>O. h. sitkensis</i>) black-tailed deer, which exhibit a complex evolutionary history shaped by survival in glacial refugia, postglacial expansion, incomplete lineage sorting, and recent introgression. These dynamics make them an ideal system for examining population responses to past climate change. However, limited temporal sampling in previous genetic studies has obscured the timing and mechanisms of postglacial dispersal, and the divergence between the two black-tailed deer subspecies remains unresolved.</p> Results <p>We analyze genome-scale data from ancient and modern deer spanning the last 13,500&#xa0;years to reconstruct the evolutionary history of Sitka black-tailed deer in Southeast Alaska. Fossil and genomic evidence supports a primary postglacial expansion from a southern refugium, with asynchronous deglaciation and fluctuating sea levels along the Pacific Northwest Coast influencing northward colonization. Early Southeast Alaska samples (~ 9.2–8.5&#xa0;cal kyr B.P.) contain mule deer mitochondrial haplotypes, indicating past contact or incomplete lineage sorting, while later individuals (&lt; 6&#xa0;cal kyr B.P.) carry Sitka black-tailed deer haplotypes, suggesting lineage turnover following mid-Holocene climatic cooling.</p> Conclusions <p>Our results reject the hypothesis of a distinct northern refugium for Sitka black-tailed deer and instead support postglacial divergence from a shared black-tailed deer refugium south of the Cordilleran Ice Sheet. The asynchronous retreat of ice and dynamic sea-level history fostered repeated dispersal pulses, localized isolation, and secondary contact, shaping the present-day genetic and morphological diversity of <i>O. hemionus</i>.</p>