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Metapopulation models typically assume that suitable habitats occupied by local populations and unsuitable matrix separating them form a ‘black-and-white’ landscape mosaic, in which dispersal is primarily determined by the spatial configuration of habitat patches. In reality, however, the matrix composition is also likely to influence dispersal. Using intensive mark-recapture surveys we investigated inter-patch movements in Maculinea (Phengaris) nausithous and M. teleius occurring sympatrically in six metapopulations. Three of these metapopulations had the matrix dominated by forest, an inhospitable environment for grassland butterflies, whereas in the remaining three the matrix was mostly composed of open environments. Dispersal parameters derived with the Virtual Migration model revealed significant differences between both groups of metapopulations. Both species had a lower propensity to emigrate from their natal habitat patches, and they suffered substantially higher dispersal mortality in the metapopulations with forest matrix. On the other hand, mean dispersal distances were roughly an order of magnitude longer in forest matrix as compared with open landscapes (ca. 500–1,500 vs. 100–200 m). Our results suggest that inhospitable forest matrix induces strong selection against dispersal, leading to a reduced emigration rate. At the same time, the selection may promote emigrants with good dispersal abilities, which are able to perform long-distance movements. Thus, while it is generally believed that a matrix structurally similar to the habitat of a species should improve the functional connectivity of habitat patches, our findings imply that this may not necessarily be the case.