Mountain ecosystems are important biodiversity hotspots and valuable natural laboratories to study community assembly processes. Here, we analyze the diversity patterns of butterflies and odonates in a mountainous area of high conservation value-Serra da Estrela Natural Park (Portugal)-and we assess the drivers of community change for each of the two insect groups. The butterflies and odonates were sampled along 150 m transects near the margins of three mountain streams, at three elevation levels (500, 1000, and 1500 m). We found no significant differences in odonate species richness between elevations, but marginal differences (p = 0.058) were found for butterflies due to the lower number of species at high altitudes. Both insect groups showed significant differences in beta diversity (βtotal) between elevations, with species richness differences being the most important component for odonates (βrich = 55.2%), while species replacement drove the changes between butterfly assemblages (βrepl = 60.3%). Climatic factors, particularly those depicting harsher conditions of temperature and precipitation, were the best predictors of total beta diversity (βtotal) and its components (βrich, βrepl) for the two study groups. The study of insect biodiversity patterns in mountain ecosystems and of the role played by different predictors contribute to further our understanding on the community assembly processes and may help to better predict environmental change impacts on mountain biodiversity.