In migratory species, the way in which conspecifics from different breeding populations are distributed during the non-breeding period is important from and ecological, evolutionary and conservation perspective, but such knowledge is still limited for most species. Migratory and sedentary blackcaps Sylvia atricapilla wintering in southern Spain can occupy two habitat types: forests and shrublands. According to earlier studies, blackcaps prefer forests over shrublands, and residents remain nearly restricted to forests. However, whether migrants with different breeding origin occupy the two habitats differently is unknown. We used morphological and biogeochemical data (hydrogen isotope ratios measured on feathers: δ2Hf), which show variation along the breeding range of the species, to answer this question. Isotope analyses supported the reliability of morphology as a method for distinguishing between migratory and sedentary blackcaps in sympatry, showing that sedentary individuals are rare in shrublands while migratory ones are abundant in both habitat types. However, migratory blackcaps scored similar δ2Hf values in forests and shrublands, and neither did vary in structural size or flight morphology between habitats. Our study suggests that migrants from a wide range of breeding origins end up mixing between forests and shrublands, which may explain the patterns of variation in space and time in the abundance of blackcaps in this area, and supports the view that inequalities may arise among migrants with the same origin but wintering in different habitats. Such inequalities might carry over into other stages of blackcaps’ life cycle contributing to the regulation of its migratory populations.