Sequences from the internal transcribed spacer region of nuclear DNA (ITS) and the trnL-F regions of chloroplast DNA for fifteen species of Chirita and seven species of Chiritopsis were used to assess phylogenetic relationships between Chiritopsis and Chirita section Gibbosaccus. Parsimony and Bayesian inference (BI) analyses were conducted using separate nuclear and chloroplast data sets, as well as a combined data set. Phylogenetic trees resulting from separate analyses proved highly congruent and the combined analysis of the two data sets produced a well-supported topology of the species and sections examined. Section Gibbosaccus proved paraphyletic and Chiritopsis polyphyletic in all analyses. Our results provide evidence that the species of Chiritopsis are embedded in section Gibbosaccus and were derived at least twice from within section Gibbosaccus. Finally, we reconsider the morphological evolution and adaptation between and within the two genera. The present analyses indicate that nomenclatural changes will be needed to reflect more accurately relationships in the Gibbosaccus-Chiritopsis complex. Only about 10% of the species in Chirita have been sampled and further data are required before any taxonomic changes can be suggested.