More than 30 collections of Tylophora from all over its geographic range were analysed together with representatives of all other genera in subtribe Tylophorinae except Rhyncharrhena. Regions of the chloroplast genome (trnT-L spacer, trnL intron and trnL-F spacer) as well as the nuclear genome (internal transcribed spacer including 5.8S of nuclear ribosomal DNA) were sequenced. Both the cpDNA dataset and the rDNA dataset yield a number of stable clades, but a completely resolved and stable phylogeny is not obtained from either alone or by combining them. The small East African and Arabian genera Blyttia, Diplostigma, Goydera and Pleurostelma form a well-supported clade in both datasets. Pentatropis is always recognized as monophyletic. Vincetoxicum is not clearly separable from Tylophora, and probably covers the temperate species, while Tylophora covers those in the tropics and subtropics.