The Tropical Andes are an important hotspot for biodiversity, with one of the greatest species richness and endemism on earth. This mega diversity is partly due to a complex biogeographic history, including rapid evolutionary radiations in many plant groups, coexisting in a large elevational gradient with a variety of habitats. In such complex conditions, including a history of elevational range shifts and secondary contact between isolated populations, it is hypothesized that hybridization among related lineages is common and could be driving rapid diversification processes in some clades. Weinmannia (Cunoniaceae), an abundant and diverse clade of woody plants, is an ideal group to explore this hypothesis as numerous related species occur across the elevational gradient, have broadly overlapping geographic ranges, and display wide variation in morphology. Previous observations have shown the existence of intermediate morphological phenotypes that do not correspond to known species and could be the product of interspecific hybridization. In this study, genome-wide SNP markers were used to 1) assess whether Central Andean species of Weinmannia delimited based on morphology form cohesive genetic groups and 2) to test for the presence of hybridization. We evaluated whether morphologically described species are consistent with patterns of genetic structure and tested for the presence of interspecific hybrids in a clade of six species with partially overlapping distributions. We genotyped 126 individuals using 2bRAD along an elevational gradient from 1,900 to 3,700 m in the Madidi National Park (Bolivia). Genetic clusters and putative hybrids were identified using STRUCTURE and PCA; then, we reconstructed phylogenetic relationships among the six species. The results showed that most species of Weinmannia delimited based on morphology were genetically distinct, but fewer genetic clusters were found than morphologically described species. Several species consisted mainly of hybrids, suggesting that taxonomists likely described hybrid populations as distinct taxonomic species. Two species, W. nebularum, and W. davidsonii were often found hybridizing, indicating weak species boundaries among these two species. Therefore, the study showed a high incidence of hybrids in Weinmmania species from the Tropical Andes. These results highlight the importance of considering hybridization and its effects on taxonomic and nomenclatural issues, as well as on the study of plant evolution in species-rich groups.