This study aimed to characterize the genetic diversity of the Passiflora genus in Colombia using molecular markers. The study: 1) Analyzed 213 Passiflora individuals representing 151 species and 15 subgenera using chloroplast and mitochondrial DNA markers. This identified 280 chloroplast and 372 mitochondrial haplotypes. 2) Chloroplast DNA provided better resolution of relationships than mitochondrial DNA, separating the Decaloba subgenus and revealing geographic structuring of some groups. 3) Results only partially agreed with morphology-based taxonomy, suggesting divergence between genomes and mixed modes of organelle transmission in the genus. The study helped elucidate the evolution and systematics of Passiflora but also highlighted remaining questions