Context <p>Human-modified environments play a crucial role in the conservation of biodiversity, but not all species exhibit the same genetic responses to anthropogenic pressures. Yet, the effect of landscape features on the genetic diversity of coexisting species, as well as their interactions, remain poorly understood.</p> Objectives <p>We evaluated how landscape features influence genetic diversity and differentiation, and if the association showed a scale of effect, of four anuran species (<i>Rhinella horribilis</i>, <i>Leptodactylus melanonotus</i>, <i>Tlalocohyla smithii</i>, <i>Smilisca baudinii</i>) across human-modified habitats.</p> Methods <p>We estimated three landscape metrics (amount of land class, configuration, heterogeneity) of different land uses (vegetation cover, water bodies, urban zones, crops/pastures) at different spatial scales, along 17 sites in Sierra Madre del Sur, Oaxaca, Mexico. We obtained ddRadSeq genomic data and estimated four metrics of genetic diversity and differentiation (<i>Ho</i>, <i>F</i>_<i>ST</i>, <i>Pa</i>, <i>F</i>_<i>IS</i>) per species per sampling site. We applied a comprehensive set of analyses to determine the best models explaining the relationship between the landscape and the species genetic patterns.</p> Results <p>Landscape configuration and heterogeneity played a significant role in explaining genetic diversity, while the scale of effect did not show clear relationships. The landscape heterogeneity, urban and crops/pastures configuration, and number and configuration of water bodies were key predictors explaining the species genetic patterns, and revealed both unique and shared patterns.</p> Conclusions <p>We identified that key landscape configuration and heterogeneity metrics influenced the genetic diversity and connectivity of the community of anurans studied across human-modified landscapes, highlighting species-environment-genetic interactions. Maintaining heterogeneous landscapes is particularly important for all anuran species, including features that enhance connectivity across different populations and sustain local ecological dynamics.</p>