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The population genetic structure of many high-latitude species in North America was affected by the last glaciation, and current structure reflects isolation in refugia and colonisation patterns. Large ice-free areas, both south of the ice sheets and in the north-west, supported numerous flora and fauna throughout this period. Fossil evidence suggests additional western glacial refugia existed both on Haida Gwaii (the Queen Charlotte Islands) and in northern Idaho. The chestnut-backed chickadee Poecile rufescens is a songbird found along the western edge of Canada and the United States, with a linear distribution along the coast, and an isolated interior population. Mitochondrial DNA sequence data (control region and ATPase 6–8) from 10 populations (n = 122) were used to test for population genetic structure. The data supported a general north/south separation. Haida Gwaii was found to be genetically distinct from the rest of the populations, and the two northern British Columbia populations separated from all but Alaska. The interior population showed evidence of both historical isolation and secondary colonisation by birds from coastal populations. Neutrality tests suggested a past population expansion in all populations from previously glaciated areas, and a stable population in areas believed to be unglaciated. This pattern supports the use of multiple glacial refugia by the chestnut-backed chickadee. We could not reject the use of Haida Gwaii or the interior (i.e. Clearwater Basin) as glacial refugia.