AbstractThe precise generic delimitation of Aliella and Phagnalon and their tribal affinities are at present unresolved. The main goals of our study were to verify the monophyly of these two genera and to determine their closest affinity group within Gnaphalieae. We analysed sequences of the trnL intron and trnL‐trnF spacer of Gnaphalieae and other Compositae tribes, in order to elucidate the tribal position of Aliella, Macowania, Phagnalon and Philyrophyllum. In addition, we analysed ribosomal nrDNA together with the ycf3‐trnS and trnT‐trnL spacers of cpDNA to elucidate the relationships within Aliella and Phagnalon. The genera Anisothrix, Athrixia and Pentatrichia are closely related to Aliella and Phagnalon. Aliella, Macowania and Phagnalon are nested within the "Relhania clade", and the subtribal affinities of Philyrophyllum lie within the "crown radiation clade". The monophyly of Aliella and Phagnalon is not supported statistically and Aliella is paraphylethic in most of the analyses. The resulting phylogeny suggests an African origin for Aliella and Phagnalon and identifies three main clades in Phagnalon, the Irano‐Turanian clade, the Mediterranean‐Macaronesian clade and the Yemenite‐Ethiopian clade. Some endemics to Yemen and Ethiopia are resolved in the Mediterranean‐Macaronesian clade, providing new evidence of phytogeographical links between Macaronesia, Eastern Africa and Southern Arabia. Incongruence between the chloroplast and nuclear molecular data and the lack of resolution in some clades may indicate that hybridization could have played an important role in the evolution and diversification of Phagnalon and Aliella.