Wood Warblers Phylloscopus sibilatrix have declined considerably throughout most of their north and western breeding range in Europe but the causes of this decline are unknown. Declines may be related to factors on the breeding grounds, stopover sites and/or wintering grounds. We used multi-isotope (δ²H, δ¹³C, δ¹⁵N) measurements of winter-grown feathers of 314 individuals breeding in the Białowieża Forest (E Poland) to infer where they wintered in sub Saharan Africa over a 4-year period from 2009–2012. We used both aspatial and spatially specific assignment techniques involving a previously developed clustering algorithm related to long-term patterns of precipitation (δ²H) and theoretical plant-based isoscapes (δ¹³C, δ¹⁵N) for Africa. We determined that our breeding population was consistently assigned to the forested region of the Congo basin. Males were more depleted in ¹³C and ²H and more enriched in ¹⁵N than females suggesting potential sexual habitat segregation on the wintering grounds. We then similarly examined less extensive samples from Wood Warblers breeding in England, Netherlands, Germany, Switzerland and Karelia (NW Russia), and found a similar assignment to the Congo basin. For all sites, males were isotopically distinct from females suggesting sex-specific habitat segregation on the wintering grounds. Our geospatial assignment model now provides a protocol for testing the hypothesis that declining populations winter more in heavily fragmented forests of west Africa compared to the Congo basin. We encourage this approach for the investigation of migratory connectivity in other sub Saharan Afrotropical migrants.