Topography and historical range expansion has formed a so-called migratory divide between two subspecies of willow warbler (Phylloscopus trochilus) in central Scandinavia. The autumn migratory directions of individuals assigned molecularly to both subspecies and possible hybrids were recorded using orientation cage experiments in southwest and southeast Sweden. We found pronounced differences in willow warblers' orientation in respect to genotype. The mean directions registered in the control experiments were in accordance with the ringing recoveries and analyses of stable isotopes for Scandinavian willow warblers. With the same individuals we performed displacement experiments between both sites. They resulted in non-significant orientation, which could be explained by the intermediate distance of the displacement or reactions to housing, transportation and location. On a separate set of birds we tested whether stress following transportation could explain the disorientation and found that orientation before and after transport was unchanged. Experimental studies of effects of intermediate displacements across longitudes and studies of orientation of hybrid individuals in the zones of migratory divides are crucial for understanding the mechanisms underlying orientation behaviour. Our work further stresses the importance of knowing the migration genotype of a particular bird under study, in order to correctly evaluate expected migration routes.