The phylogenetic relationships of six out of seven genera from the informal Hinterhubera group (Hinterhuberinae) and nine other subtribes in tribe Astereae primarily with Southern Hemisphere distributions were studied using internal and external transcribed spacer region nuclear DNA (ITS and ETS) sequence data. Bayesian and parsimony analyses were conducted on both datasets, independently and combined. Topologies resulting from the ITS and combined data sets were highly congruent, while the ETS based phylogenies were poorly resolved, probably because the characters are fewer and less informative. The monophyly of the Hinterhubera group was not confirmed, nor were the monophyly of the subtribes Podocominae, Lagenophorinae, Grangeinae, and Asterinae as delimited by Nesom and Robinson. Instead, our results suggest a closer relationship among the taxa from similar geographic areas. Within the Hinterhubera group, the monophyly of the genera has been confirmed. Westoniella was sister to Laennecia (Podocominae), while Hinterhubera was sister to Laestadia and Blakiella. The radiate Diplostephium and Guynesomia were disparately placed in the southern hemisphere clade and not related to the other radiate genera of Hinterhuberinae. Present analyses suggest that dioecy in Aztecaster and Baccharidinae evolved independently as hypothesized by Nesom. Archibaccharis (Baccharidinae) was sister to Plagiocheilus (Grangeinae). The analyses of ITS and ETS data, and Bayesian analysis of the combined dataset, resolved Baccharidinae as non monophyletic. Constraint analyses forcing a monophyletic Baccharidinae, with Plagiocheilus sister to Archibaccharis, did not reject monophyly of the subtribe.