We adopted a landscape-scale approach to analyze the genetic patterns (diversity, structure, and differentiation) of the Marbled White (Melanargia galathea). This butterfly species is characteristic of semi-dry grasslands, which have substantially declined in Switzerland during past decades. We sampled individuals on a regular grid of the established Biodiversity Monitoring program of Switzerland over five consecutive years, obtaining 1639 genotyped individuals from 185 locations. Results showed that M. galathea populations cluster into five spatially aggregated clusters that largely coincide with the biogeographic regions of Switzerland. Genetic diversity (allelic richness) was higher in the South of the Alps, likely related to immigration dynamics that suggest recolonisation from the South after the last glaciation. Demographic history resulted in distinct isolation by distance (IBD) and by cumulative elevational difference (isolation by altitude, IBA) at large scale, while regional IBD and IBA were less pronounced. This pattern was likely induced by the barrier effect of the high mountains of the Alps impeding continuous northward migration after the last glacial maximum. A temporal analysis revealed that regional genetic diversity did not change strongly during the five sampling years. This result indicates that the genetic diversity pattern in M. galathea has not been noticeably affected by historical land-use change or that the sampling period of five years is too short to detect any changes. Our findings highlight the regionally, topography-induced distinct genetic clusters, relevant for consideration as conservation units and likely reflecting genetic structures similar to those found in other butterfly species of conservation concern.