1) Background: Neotropical montane forests represent one of the most diverse ecosystems; however, they are also the most threatened for deforestation. Our main goal is to evaluate the change in Basal Area (BA), Density and Species Composition of montane forests in the southern Ecuador and to determine the influence on some critical ecological and geomorphological factors. 2) Methods: One hundred thirty-two temporary plots of 400 m² each were installed; we identified and measured all trees> 10 cm DBH. We modeled species diversity (Fisher’s alpha) change in relation to climatic, elevational and geomorphological gradients with GLM and Kruskall-Wallis analyses. The change in composition was determined using Cluster Analyses (BIOENV analysis followed by a LINKTREE procedure). Non-metric multidimensional scaling (NMDS) was used to analyze changes across climatic and geomorphological gradients. Finally, we used SIMPER analysis to identify the species that contributed most to the dissimilarity among the different elevations. 3) Results: Formation of floristic groups was influenced by altitude, temperature and Isothermality; physiographic province, great landscape, geological landscape and lithology. Plots located in low hills have higher alpha diversity with respect to the high hills and dissected mountains. 4) Conclusions: The elevation is first hierarchical factor responsible of the division of structural and floristic groups. Plots located on the whitish tuff have a higher alpha value diversity compared with plots in andesitic tuffs. Wettest quarter (> 839 mm) and Isothermality (> 90.5) are the climatic factors that driven de floristic divisions.