Phylogenetic relationships of Passiflora subgenus Decaloba were examined using 148 taxa and four molecular markers: nuclear nrITS, ncpGS, cp trnL-F, and ndhF. Relationships of subgenus Decaloba to the other four Passiflora subgenera (Astrophea, Deidamioides, Tetrapathea, and Passiflora) are investigated, as are relationships among the eight supersections within subgenus Decaloba. Results indicate that subgenus Deidamioides is not monophyletic. Subgenus Astrophea subgenus Deidamioides (section Tryphostemmatoides) together form the most basally branching lineage in the genus, followed by a clade comprised of subgenus Passiflora subgenus Deidamioides (sections Tetrastylis, Polyanthea, and Deidamioides). Passiflora obovata (subgenus Deidamioides section Mayapathanthus) is resolved as part of subgenus Decaloba. The Old World subgenus Tetrapathea is supported as sister to subgenus Decaloba. Subgenus Decaloba is monophyletic and contains seven major lineages that generally correspond to currently recognized supersections. Within subgenus Decaloba, supersection Pterosperma is most basally branching, followed by supersection Hahniopathanthus P. obovata. The New World species Passiflora multiflora, the type of supersection Multiflora, is resolved as sister to a monophyletic Old World supersection Disemma. The remainder of the former supersection Multiflora is paraphyletic with respect to supersection Auriculata. Supersections Cieca, Bryonioides, and Decaloba are monophyletic. Within supersection Decaloba, two main clades are resolved: 1) section Xerogona section Decaloba pro parte and 2) the remainder of section Decaloba. The molecular phylogeny supports a New World origin for Passiflora, with two independent radiations to the Old World. Morphological synapomorphies are discussed for the major clades, documenting a pattern of remarkable evolutionary lability in several notable characters.