The genus Dahlia presently consists of 35 species, primarily from Mexico. Species are usually placed in four sections: Pseudodendron, Epiphytum, Entemophyllon, and Dahlia, based largely on morphological characters, supplemented with cytological, geographical, and biochemical data. Combined molecular sequence data from both the internal and external transcribed spacer regions (ITS and ETS), located within the nuclear ribosomal gene repeat unit, are used to infer a phylogeny of the genus. Section Entemophyllon forms a very well-defined clade based on these data. Dahlia merckii and D. tubulata are positioned between sect. Entemophyllon the remaining taxa. Sections Pseudodendron and Epiphytum are closely allied with each other and a few species from sect. Dahlia to form the variable root clade (VRC), which incorporates all species with unusual underground structures, along with some species exhibiting the more typical tuberous type. The remaining species of sect. Dahlia form a well-defined clade, the core Dahlia clade (CDC).