<p>Dispersal is a fundamental ecological process, promoting long-term resilience by maintaining functional connectivity among populations. At the community level, the interaction between life history traits and landscape features results in different patterns of connectivity among species, with implications for (meta)community resilience and viability. Comparative studies assessing the effects of different landscape elements and land uses on patterns of gene flow on co-distributed species thus provide key information for the management of biotic communities. We carried out a comparative landscape genetics study in two Ibero-Mediterranean regions with contrasting landscapes (dominated by forests and agricultural plots, respectively), focusing on three amphibian species differing in key life history traits: Iberian tree frog (<i>Hyla molleri</i>), Iberian green frog (<i>Pelophylax perezi</i>) and western spadefoot toad (<i>Pelobates cultripes</i>). We used 15–16 DNA microsatellite markers to characterize patterns of genetic diversity and structure among species and regions, finding signs of population structure in forested areas despite shorter geographic distances among populations than in agricultural areas, which were characterized by weaker genetic structure. The optimization of landscape resistance surfaces revealed that open areas associated with crops, alongside meadows and riparian vegetation, promote gene flow in all species in both regions, whereas landscapes composed of closed forests and scrub offered reduced connectivity. Landscape genetics results thus support an important role of traditional agro-livestock areas in favoring amphibian connectivity in Mediterranean ecosystems. We discuss the implications of these results for the conservation of diverse amphibian assemblages in landscapes subjected to intense transformation by human activities.</p>