The reciprocal monophyly of Craspedia and Pycnosorus (Asteraceae, Gnaphalieae) is tested, with a phylogenetic analysis of ribosomal and chloroplast DNA. Although one species of the latter genus was not sampled, the results of the present study indicated that it is most likely monophyletic as opposed to paraphyletic with respect to Craspedia. Within Craspedia, deeper sampling results in the appearance of several species (C. aurantia, C. coolaminica, C. glabrata and C. variabilis) in both major Australian rDNA clades, indicating that the available molecular phylogenies have to be considered gene trees instead of species phylogenies. Additional studies using more independent loci and species-tree approaches are needed to resolve species relationships in the genus.