Habitat loss and fragmentation are among the greatest threats to biodiversity since unsuitable habitat can be a significant barrier to gene flow, disrupting the connectivity of populations. In this scenario, landscape genetic approaches have been applied as invaluable tools to demonstrate how contemporary habitat alterations affect gene flow. In this study, we used nine microsatellite genotypes to determine the landscape features driving genetic diversity, structure, and functional connectivity among eleven sampling sites of a micro-endemic, and critically endangered salamander (Pseudoeurycea robertsi) in the Nevado de Toluca Volcano. We also modelled the ecological niche of P. robertsi to assess the most important habitat features associated with its probability of presence and analyzed the corridor network to identify important core areas and corridors to keep the network connected, as well as points where the network connection is lost or tightened. Moreover, we performed a redundancy analysis to assess the effect of genetic distance and habitat resistances on gene flow.We found the highest levels of genetic diversity and connectivity at the northwestern part of the Volcano. Meson Viejo sampling site was of especial importance to overall network connectivity. We found low levels of migration rates and low levels of genetic structure. The most important habitat feature associated with probability of presence of Pseudoeurycea robertsi was the Abies forest, and two models were significant under the RDA analysis: Abies forest and Abies forest+Grasslands. We recommend prioritizing the areas of the northwestern and central parts of the volcano in conservation programs.