Established concepts of Chrysothamnus have been primarily based on morphological similarity or on molecular studies employing only exemplar taxa. Those investigations and treatments conceptualized Chrysothamnus as a single evolutionary unit with affinity for Ericameria, Petradoria, and Stenotus among other taxa. The hypotheses of relationship presented here are based on nuclear ribosomal 3′ ETS and ITS data that were analyzed using several optimality criteria. The results indicate that Chrysothamnus as traditionally perceived is polyphyletic, with species placed in four well-supported lineages. Three of the four clades also contain taxa from other genera. Seven species of Chrysothamnus along with Acamptopappus, Amphipappus, Hesperodoria scopulorum, Tonestus lyallii, and Vanclevea constitute one clade, while four species aggregate in another clade that includes Hesperodoria salicina, Tonestus microcephalus, and T. peirsonii. A third lineage consists of Chrysothamnus gramineus and appears distantly related to any other Chrysothamnus. Finally, four species of Chrysothamnus recently transferred to Ericameria are strongly supported within the Ericameria lineage. Stenotus and Tonestus as traditionally circumscribed are not supported by the molecular data. Instead, the generitype of each is aligned with taxa other than species presently included within the same genus. The results of this investigation indicate that some of the morphological features used to delimit these genera may be the product of convergence, thus diminishing their value for phylogenetic reconstruction.