We derive detailed relationships among and within the African Penaeaceae, Oliniaceae, Rhynchocalycaceae, and Central and South American Alzateaceae based on six chloroplast data sets that include sequences of all genera and most species. This is the first study addressing intrafamilial relationships of Penaeaceae and Oliniaceae based on molecular data. All analyses conducted on the six separate and combined data sets produce similar tree topologies without any major conflicts. The resulting phylogenies suggest that the monospecific New World Alzateaceae is sister to the three African taxa and that the monospecific Rhynchocalycaceae is sister to Oliniaceae/Penaeaceae. Within Penaeaceae, our results partially contradict traditional generic circumscriptions, suggesting, for example, that Brachysiphon and Stylapterus are paraphyletic. Within the monogeneric Oliniaceae the analyses reveal two well‐supported clades. We also performed comparative studies of floral development and morphology of Penaeaceae, Oliniaceae, and Rhynchocalycaceae. We analyze the results of these comparativel studies in the context of the molecular phylogeny to test competing hypotheses of perianth organ homology in Penaeaceae and Oliniaceae. Our analyses show that flowers of both families are most parsimoniously interpreted as having an obhaplostemonous organization. The respective homology of calyx and corolla among the three families is further supported by congruent patterns of floral development and structural similarities including anatomical and histological features.