There have been numerous recent observations of changes in the behavior and dynamics of migratory bird populations, but the plasticity of the migratory trait and our inability to track small animals over large distances have hindered investigation of the mechanisms behind migratory change. We used habitat-specific stable isotope signatures to show that recently evolved allopatric wintering populations of European blackcaps Sylvia atricapilla pair assortatively on their sympatric breeding grounds. Birds wintering further north also produce larger clutches and fledge more young. These findings describe an important process in the evolution of migratory divides, new migration routes, and wintering quarters. Temporal segregation of breeding is a way in which subpopulations of vertebrates may become isolated in sympatry.