<p>The alarming decline in bee populations throughout the world makes it imperative to understand the dynamics of its communities in undersampled tropical regions such as Colombian Choco and Amazon. Euglossine bees, also known as orchid bees, are the primary pollinators of orchids in the Neotropical region, and little is known about the resilience of these communities to geographical formations. Combining phylogenetics with the community ecology makes it possible to evaluate the evolutionary relationships among coexisting species, and to associate the phylogenetic structure of the community with the niche overlap and historical events. Here, we evaluated whether the orchid bee communities differ phylogenetically by altitudinal range on each side of the Andean mountains. We collected euglossine bees using chemical attractants at three different elevation levels in two sites (Putumayo and Nariño) separated by the Andean cordillera. We captured 1225 bees belonging to 64 species and four genera. We found phylogenetic clustering in Low and High Nariño, in contrast to Putumayo and Mid Nariño, which tended toward a random draw. However, overdispersion was not recorded; hence, the role of environmental filtering and competitive exclusion in community assembly along elevation gradients remains unclear. Consequently, we propose that the emergence of the Northern Andes generated changes in the composition of orchid bee communities distributed sympatrically. The niche conservatism observed in Nariño is explained by the narrow zone and climatic homogeneity and randomness in Putumayo, by the extension of the territory and other geological events such as Pleistocene refugees and Amazon River formation.</p>