Cnidoscolus (Euphorbiaceae) is an American genus of 99 species, distributed from the United States to Argentina and the Antilles. The genus is noteworthy due to the presence of stinging hairs, a feature otherwise very rare in Euphorbiaceae. Here we constructed a phylogenetic hypothesis for relationships in Cnidoscolus using both nuclear (ITS) and chloroplast (psbA-trnH, trnL-trnF) markers. We included 44 species and 7 additional subspecies (of 4 species), which represent a broad geographic and taxonomic sample of the genus. The nuclear and chloroplast datasets were analyzed separately. Various incongruencies were detected between the nuclear and plastid phylogenies, and in general, the ITS reconstruction is better resolved and has more clades that are highly supported. In both analyses, Cnidoscolus is confirmed to be monophyletic and composed of two major lineages: a northern clade that comprises species distributed primarily in North and Central America and a southern clade composed of mostly South American species. We conducted ancestral reconstructions of three characters important in the classification of the genus: (1) primary leaf venation, (2) number of staminal whorls in the androecium, and (3) petiolar glands. Based on morphology and the molecular phylogeny, we propose an updated infrageneric classification that recognizes eight sections and two subsections, and we place 98 of the accepted species into this new classification, with one species' position uncertain.