In this study we explore the phylogenetic relationships within the hummingbird genera Doryfera, Schistes and Colibri (Family Trochilidae), distributed in the Andes, the Pantepui, the southern Brazilian uplands and the lowlands of South America including the Choc, the Amazon Basin, the Chaco, the Cerrado, and the southeastern Brazilian coast, as well as Central and Mesoamerica. To do this, we included a comprehensive sampling of the 16 traditionally recognized subspecies within this group. We found that Doryfera, Schistes and Colibri form a well-supported monophyletic group, and that most of the traditionally recognized subspecies are indeed evolutionary lineages. As there is a high likelihood that the ancestors of this clade of hummingbirds were distributed in the lowlands, we ask: what events might account for the diversification of this subclade of mangoes into the Andes with a later potential dispersal episode from the Andes to the lowlands? We found that several phenomena such as the uplift of the Andes, the marine transgressions of the Plio-Pleistocene, the final closure of the Isthmus of Panama and the climatic oscillations of the Pleistocene might be at least, in part, responsible for the diversification of this group in both the lowlands and the highlands of this region of South America.