The exine ultrastructure of 18 species of Anisopappus (Anisopappinae, Athroismeae, Asteraceae) and three species of Duhaldea (Inuleae, Asteraceae) was studied using transmission electron microscopy (TEM). Two ultrastructural patterns were identified: senecioid and helianthoid. The senecioid pattern is characteristic of the species included in the basal clades of the phylogenetic tree of Anisopappus, as published in earlier studies. The helianthoid pattern is restricted to the taxa placed in the derived clades, including the core group of species of Anisopappus in which A. chinensis, the type species, is included. The observed ultrastructural differences seem to suggest that a future splitting of Anisopappus into several different genera should not be disregarded and that the helianthoid pattern represents, within this genus, the derived condition. The ultrastructure of the exine supports the inclusion, suggested by previous authors, of the species Duhaldea stuhlmannii, but not that of Philyrophyllum schinzii, in Anisopappus. In contrast, the three studied species of Duhaldea (D. cappa, D. nervosa, D. revoluta) present an exine with a senecioid pattern, which is characteristic of the tribe Inuleae, in which they are included. The ectoaperture, mesoaperture, and endoaperture of all studied Anisopappinae and of Duhaldea respectively intersect the tectum plus columellae, the foot layer and the outer part of the endexine, and the inner part of the endexine. This feature seems to characterize, in a consistent way, the ‘Heliantheae alliance’, and is also present in all the studied Asteroideae (except Anthemideae), Dicomoideae, and Carduoideae.