The pantropical family Melastomataceae is one of the top 10 families worldwide in terms of species richness, demonstrating some of the highest speciation rates within the angiosperms. Within the Neotropics, generic limits and species relationships are still unclear across many different clades. The genus Chaetogastra DC., with ca. 120 species, represents a significant Neotropical radiation where generic limits and species relationships remain problematic. Most species of Chaetogastra and close relatives were formerly treated as Tibouchina s.l., which in turn are closely related to the genera Andesanthus, Heterocentron, Monochaetum, and Pleroma. Chaetogastra has a wide distribution from Mexico to Central America, the West Indies, northern South America, across the Andes, Paraguay, Uruguay, and a great number of species occur in Brazil. We carried out a phylogenomic analysis using both plastome and HybSeq data to try to resolve species relationships within Chaetogastra and generic relationships among close relatives. We sampled broadly across Chaetogastra and closely-related genera and likewise we added publicly available sequences from Genbank. We performed Maximum likelihood inference and Bayesian analysis for the plastome data and the pseudo-coalescence method ASTRAL for species using our nuclear dataset to test our hypothesis of patterns of speciation and divergence in both genomes. Comparative phylogenomic analyses using both the plastome and nuclear probe set allowed us to test topological differences among species and generic relationships. Furthermore, we were able to gain insights about the evolution of Chaetogastra as it relates to the Andean uplift in South America, as compared with other radiations in that region.