Forests have been globally reduced due to unprecedented rates of deforestation and habitat transformation, which in turn affects the species’ genetic structure. Despite harboring a high endemism, temperate forests are the second most degraded terrestrial ecosystem in Mexico. Therefore, understanding the spatial genetic patterns is fundamental to implement management and conservation efforts that contribute with their long-term persistence. By using Single Nucleotide Polymorphisms, this study evaluated the fine-scale spatial genetic structure and the effect of landscape features on gene flow of two conifers, Abies religiosa and Pinus montezumae, each with different successional affinity, in a temperate forest of central Mexico exhibiting high landscape heterogeneity due to topography and land-use changes. Based on successional affinity of species we expected isolation by resistance in Abies religiosa and a panmictic population in Pinus montezumae. We analyzed the genetic structure and the effects of altitude, Aspect and land-use changes on the genetic connectivity patterns. A weak isolation by distance pattern was detected in A. religiosa, while the spatial component explained only the 3% of its genetic variation. In P. montezumae, a very low structure signal was detected between slopes. Overall, the analyses revealed an absence of genetic structure in both species, i.e., no landscape predictor had an effect on gene flow between the populations. We recommend increasing the spatial extent and the assessment of more environmental predictors to further support the study of genetic structure patterns in the species studied. Our study contributes with information for the conservation of Mexican temperate forests.