The Haida Gwaii archipelago (formerly the Queen Charlotte Islands) off northern British Columbia hosts many endemic taxa of plants and animals, including 9 endemic subspecies of birds. Genetic studies suggest that some of these taxa originated in a glacial refugium in the area, whereas other taxa apparently arose after the recession of the glaciers. The Orange-crowned Warbler (Vermivora celata) is a Nearctic—Neotropic migrant passerine broadly distributed across North America. To gain insight into the importance of historical fragmentation versus recent differentiation in diversification of the Haida Gwaii avifauna, we analyzed geographic variation in 8 microsatellite loci and the mitochondrial control region among Orange-crowned Warblers from 7 breeding localities, including 2 of the 4 currently recognized subspecies (V.c. celata and V. c. lutescens). We found modest genetic differentiation among populations, with an isolation-by-distance pattern among western populations and significant differentiation between subspecies. Results from several analyses indicate that differences between Haida Gwaii and other western populations arose through restrictions in gene flow after the recession of the glaciers. Thus, patterns of genetic diversity in western Orange-crowned Warbler populations do not provide evidence that the species persisted in a Pleistocene refugium in the area of Haida Gwaii.