<p>Understanding how topographical and environmental features influence population genetic structure is pivotal in ecology, evolution and conservation. Landscape genetics allows to perform such inference, along with identification of ecological corridors and barriers to dispersal. Yet, results are often constrained by the spatial scale of analysis, making generalization difficult, especially for widespread species with broad ecological niches. Comparative assessments of landscape connectivity in heterogeneous study areas can help identify elements with general impacts on population connectivity as well as idiosyncratic features with leverage only on certain types of habitats, providing key information for the design of context-dependent conservation measures. We assessed functional connectivity in a widespread but declining amphibian, the Iberian Common Toad (<i>Bufo spinosus</i>) in two areas of central Spain with contrasting landscape features: the Guadarrama foothills and the Alcarria plateau. We genotyped &gt; 500 individuals from 33 sites with 11 microsatellites and characterized genetic diversity and structure in both areas. We conducted landscape genetic analyses to reveal the differential importance of landscape features in population connectivity across study areas. We found consistent patterns, with temporary streams and moderate slopes facilitating gene flow, while major rivers and highways acted as barriers, especially in the Alcarria plateau, where population structure was more pronounced. Land cover variables partly explained patterns of functional connectivity, but their effects varied across regions, with different land classes facilitating or disrupting gene flow. Our results underscore the importance of comparative landscape genetics studies for the design of tailored conservation measures in widespread species.</p>