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Understanding the influence of human-induced changes on the evolutionary trajectories of populations is a fundamental problem [1, 2]. The evolution of reproductive isolation in sympatry is rare, relying on strong selection along steep ecological gradients [3–7]. Improved wintering conditions owing to human activities promoted the recent establishment of a migratory divide in Central European blackcaps (Sylvia atricapilla) [8, 9]. Here, we show that differential migratory orientation facilitated reproductive isolation of sympatric populations within <30 generations. The genetic divergence in sympatry exceeds that of allopatric blackcaps separated by 800 km and is associated with diverse phenotypic divergence. Blackcaps migrating along the shorter northwestern route have rounder wings and narrower beaks and differ in beak and plumage color from sympatric southwest-migrating birds. We suggest that distinct wing …