The genetic characteristics of neutral loci in natural populations are shaped by the interplay between genetic drift and gene flow that themselves result from key ecological and evolutionary processes. Because of their influence on population size, habitats characteristics may influence substantially populations' genetic characteristics. However, past studies focused primarily on variables related to habitat quantity while habitat quality was largely overlooked. We therefore combined genetic data to detailed habitat descriptions of three sympatric butterfly species having different ecological needs to quantify the relative contribution of geographic distance and habitat quality/quantity on their genetic characteristics. In all species, the genetic diversity was greater in larger and good quality patches. The genetic differentiation of Lycaena helle (specialist species with limited dispersal) was mostly explained by geographical distances. This effect was dampened by habitat quality as populations inhabiting low quality patches had higher genetic differentiations indicating that the constraints set by local environmental factors increased genetic drift. In Boloria eunomia (specialist species with greater dispersal), the genetic differentiation was only influenced by geographic distance. Finally, in Brenthis ino (more generalist species with greater dispersal), isolation-by-distance was weak and habitat characteristics were unrelated to genetic differentiation. The different effect of habitat quality on these species' genetic characteristics suggests that fundamental ecological traits underpin their response to habitat degradation. In L. helle, a species with major conservation concerns, these results show that preserving habitat quality and connectivity among populations' are important to ensure the maintenance of fully functional metapopulations.