The Yellow Wagtail Motacilla flava consists of about 18 taxa whose taxonomic relationships are unclear. Some authors elevate 11 taxa to species based on often characteristic nuptial plumages of males, whereas others recognize two species based on molecular data. Hybridization is a regular event but with intriguingly varying intensity between different taxa. In spite of breeding generally in damp fields, their breeding habitat is actually rather diverse, which offers an opportunity for ecological segregation by breeding habitat. Indeed, some authors describe habitat differences between taxa but others do not. Two sympatrically occurring taxa are thunbergi and beema in European Russia and Western Siberia. In this study we describe their breeding habitat and determine whether this differs between taxa. We aimed to determine whether breeding habitat could be an ecological factor for sub-specific segregation in this part of their breeding range. We found strong indications for segregated breeding, despite the rather limited dataset: thunbergi occurred in bogs as a breeding bird and beema was dominantly found breeding in floodplain meadows. On one location bog and floodplain were separated by only 1.5-2 km of forest, yet here too only thunbergi occurred on the bog and beema on floodplain meadows. Following recent molecular taxonomic findings our thunbergi might very well concern plexa, belonging to the eastern species. As beema is assigned to the western species, the observed spatial segregation between plexa and beema may be representative of habitat separation of the western and eastern species in areas where they occur sympatrically. Large scale segregated breeding due to different habitat preferences could have consequences for taxonomic interpretations within the M. flava complex.