Pleistocene climatic oscillations have resulted in high rates of speciation. Lesser known are speciation events related to recent glacial retreats. During the early Holocene many Alaskan coastal glaciers receded, exposing much of the Kodiak Island Archipelago (KOD), the Kenai Peninsula, and Prince William Sound (PWS). Using fecal DNA analyses on samples collected in KOD, PWS, Kenai Fjords National Park (KEFJ), Katmai National Park and Preserve (KATM), and Vancouver Island, British Columbia (BC), we found isolation by distance to be an important mechanism for the divergence of populations of river otters (Lontra canadensis (Schreber, 1777)) along the Pacific coast. Nonetheless, our results also demonstrated that KOD river otters appear to be more isolated genetically from their mainland conspecifics (approximately 50 km away), as river otters inhabiting PWS are from those in BC (over 2500 km away). In addition, KATM and KOD otters likely differentiated from one ancestral stock that inhabited the southwestern shores of Alaska during the Pleistocene and was isolated from more easterly populations by distance. The low genetic diversity among KOD river otters, compared with similar subpopulations in PWS, is likely the result of a founder effect and limited gene flow among the different islands within the Archipelago. Our observation that glacial retreat, rising sea levels, and formation of the Gulf of Alaska Coastal Current in the early Holocene likely led to divergence of populations of river otters, a highly mobile semiaquatic mammal, highlights the potential for future speciation events related to current climate change and ocean currents in coastal animal populations.