AimThe factors that influence the diversity of Yungas Andean forest remain unexplored. Our study seeks to investigate the impact of key isolating factors on the genetic structure of multiple taxa, testing for four hypotheses: isolation by distance (IBD), isolation by resistance due to topography (IBRtopo), isolation by resistance due to habitat suitability (IBRsuit) and isolation by environmental dissimilarity (IBE).LocationYungas Andean forest.TaxonTetrapoda.MethodsWe analysed a dataset consisting of 477 Cyt‐b sequences from 138 localities, encompassing 13 species. Through multiple matrix regression, Moran Spectral Randomization of Mantel and GDM analyses, we tested the impact of each extrinsic predictor on observed genetic variation and determined the effect size of environmental variation on genetic divergence. Additionally, we investigated the spatial distribution of lineages within the study species.ResultsThe genetic variation within the Yungas exhibited varied responses that correspond to the regional landscape heterogeneity. We identified different isolating factors as the main predictor for specific species: IBD for Akodon spegazzinii; IBRtopo for certain small mammals' species; IBE for Thylamys cinderella and Oligoryzomys brendae; and IBRsuit for Calomys fecundus, Oreobates barituensis and Melanophryniscus rubriventris with some considerations. Furthermore, our results support the presence of a latitudinal pattern in the distribution of genetic lineages.Main ConclusionsThe heterogeneous landscape of the Yungas Andean forest posed varied effects on genetic variation. The effect of topography and continuity of suitable habitats over vertebrate dispersal shapes the genetic diversity, in particular topography acts either as a barrier or as corridor, while habitat suitability resistance mainly shapes endemism genetic structure; local climate represents a strong genetic promoter in transition zones; and the effect of geographic distance is less evident when considering other landscape promoter of genetic divergence. This reinforces the understanding that the complex interplay of environmental and historical factors contributes to the observed patterns of genetic diversity in this region.