Hybrid zones are often found in areas where the environmental characteristics of native habitat of both parental species meet. One of the plausible mechanisms that maintain species distinctiveness, or limit hybridization, is the existence of local species-specific preferences for the natal habitat type. We evaluated this hypothesis for two passerine bird species, the pied Ficedula hypoleuca and collared flycatcher F. albicollis, in their narrow hybrid zone in Central Europe. Both species have quite distinct habitat distributions, and they have also been reported to differ in their foraging niches. In a series of aviary experiments, we demonstrated that both species show distinct preferences for trees from their native area. The pied flycatcher preferred coniferous vegetation, while the collared flycatcher favored deciduous vegetation. In addition, both species differed in foraging substrate preferences. The pied flycatcher preferred to forage in the lower strata on the ground than the canopy, whereas the collared flycatcher foraged more at the canopy level. Both males and females of each species were highly consistent in their preference patterns. Due to the widespread nature of hybrid zones as places with transitional habitat features and the well-known habitat tight associations of various animal taxa with particular habitat types, we propose that habitat preferences might be an important and common mechanism that enhances the formation of conspecific pairs.