The Rusty Blackbird (Euphagus carolinus) has declined dramatically across its range in North America since at least the 1960s, but the causes for this decline are unknown. We measured ratios of stable hydrogen isotopes (δD) in feathers collected from Rusty Blackbirds wintering in the Mississippi Alluvial Valley (n = 255 birds) and the coastal plain of South Carolina and Virginia (n = 281 birds), 2005–2009, to estimate the region of origin of birds wintering west and east of the Appalachians, respectively. We also measured δD values in feathers from all available museum specimens collected from 1879 to 1990 in these same two regions (n = 190 birds). Isotopic values support migratory connectivity in this species with breeding populations in the western and central boreal forest migrating through a central or Mississippi flyway and those breeding in the eastern boreal forest migrating to a winter range east of the Appalachians. We detected little long-term change in the breeding origins of modern and historical populations wintering east and west of the Appalachians. However, we found short-term temporal variability in the breeding origins of birds wintering on the coastal plain from 2007 to 2009. The migratory divide suggests that efforts at management should be tailored to at least eastern and western subpopulations on both the breeding and wintering grounds. Our approach can be applied to a broad range of migratory species in North America and on other continents.