Long-distance migrants with transcontinental breeding ranges are of particular interest for the study of local adaptation and geographic differentiation in birds. We compared phenotypes and genotypes between Far East Siberian Willow Warblers Phylloscopus trochilus yakutensis Ticehurst, 1935 with the European subspecies P. t. trochilus Linnaeus, 1758 and P. t. acredula Linnaeus, 1758. We found significant differences in mean body size and plumage colour, but intra-population variation overlapped extensively between the European and Siberian populations. We used stable isotope composition in winter-grown flight feathers as a proxy for wintering sites and found differences between all three subspecies, indicating different wintering grounds. Out of four nuclear loci analyzed (three of which are known to be substantially divergent between the European subspecies), none allowed to seperate East Siberian yakutensis from North Scandinavian acredula. Hence, neither phenotypic traits nor the currently available genetic resources provide diagnostic criteria for confidently assigning individual Willow Warblers to a particular subspecies. Despite extensive overlap in phenotypes and genotypes, we propose that the subspecies names can still be used as biogeographical references to the three Willow Warbler populations that differ in migration strategies. We propose to use yakutensis for Willow Warblers breeding east of the Ural Mountains that presumably initiate autumn migration towards the southwest or west, in contrast to the genetically most similar acredula that start autumn migration towards the southeast or south. Future field studies are needed to elucidate whether the longitudinal variation in phenotype is a cline, or whether a clear contact zone between these subspecies can be identified.