The marine migratory routes of most diadromous fishes are poorly known, with the oceanic phase of their life histories often considered a black box in analyses of population dynamics. We report on the effective use of natural chemical tags in otoliths to identify origins of a North American anadromous clupeid (Alosa sapidissima). Chemical signatures were based on combined elemental and isotope ratios in otoliths and water samples taken from all 20 major spawning populations across approximately 2700 km of coastline and 19 degrees of latitude. Signatures were highly distinct, with an average classification accuracy of 93%. These signatures allowed us to estimate mixed-stock compositions of one-year-old marine migrants and provided stage-specific information about the distributions of immature fish. Mixed-stock compositions were dominated by only two to three rivers for all collections and there was a distinct lack of southern populations in the mixtures. Estimates of mixed-stock compositions for these immature fish differ significantly from those reported for older age classes. These patterns suggest this species may exhibit ontogenetic niche shifts in their migratory strategies after their transition to marine habitats.