Glacial cycles in the late Pleistocene played a dominant role in sculpting the evolutionary histories of many high-latitude organisms. The refugial hypothesis argues that populations retracted during glacial maxima and were isolated in separate refugia. One prediction of this hypothesis is that populations inhabiting different refugia diverged and then, during interglacial periods, rapidly expanded into deglaciated regions. The range of the gray wolf (Canis lupus) was modified by these expansion and contraction cycles in the late Pleistocene. Our analyses of variation of mitochondrial control region sequences corroborate previous microsatellite analyses supporting independent evolutionary histories for Coastal and Continental wolves in North America. Coastal wolves represent the remnants of a formerly widespread and diverse southern clade that expanded into coastal Southeast Alaska, likely in the early Holocene. In contrast, extant northern Continental populations appear to be admixed, composed of lineages independently arising from ancestors that persisted in either southern or northern (Beringia) refugia. This pattern of diversification suggests the possibility of 3 temporally independent colonizations of North America by wolves from Asia. Coastal wolves are the last vestige of a formerly widespread phylogroup that largely was extirpated in North America by humans during the last century. The independent phylogeographic history of these Coastal wolves has yet to be characterized. Their distinctiveness among North American wolf populations may warrant a reevaluation of their conservation status and management.