Abstract Phylogenetic relationships for the genus Calliandra section Androcallis (Fabaceae) were reconstructed, including previously sequenced species from Central and South America and unexamined species from Colombia, one of Calliandra main diversity centers. Here, we generated novel DNA sequences of Calliandra species from Colombia for the nuclear Internal Transcribed Spacer ( ITS) and the chloroplast trnL and trnL-F intergenic spacer. By incorporating a broader taxonomic sampling, the relationships among main clades in Androcallis were clarified, providing a systematics framework in which to test evolutionary hypotheses. Phylogenetic analysis recovered five well-supported clades within Androcallis . Most species within each clade had similar geographical distributions and relationships between the five major clades are strongly supported for the first time. However, core Androcallis relationships, including most species from Colombia sequenced here, remain unclear. A second goal of this study was to determine the taxonomic status of Calliandra medellinensis . This enigmatic taxon emblematic of Medellín, Colombia, is found in limited numbers within the Aburrá Valley and has been proposed to be a hybrid taxon. Here, C. medellinensis , C. magdalenae and C. haematocephala were not monophyletic within the core Androcallis clade. This suggests that C. medellinensis could potentially be an interspecific hybrid between C. magdalenae and C. haematocephala , thus challenging the taxonomic status of this species; however, more informative molecular markers should be used in future studies. Specifically, genomic studies should assess interspecific hybridization demographic models. Such insights can illuminate the C. medellinensis origin, guiding conservation strategies and providing valuable evolutionary overviews.