Croton section Pedicellati is described, with a disjunct distribution in Mexico and South America. It is recovered sister to Croton section Lamprocroton in Bayesian, Maximum Likelihood, and Maximum Parsimony analyses of nuclear ITS and chloroplast trnL-F DNA sequence data. Two new subsections, Croton subsection Lamprocroton and Croton subsection Argentini, are recognized within Croton section Lamprocroton. These well-supported sister clades include species with bifid and multifid styles, respectively. Croton breedlovei, a new lepidote species of section Pedicellati, endemic to Chiapas, Mexico, is described. Croton breedlovei is morphologically and phylogenetically closer to other lepidote species from Brazil than it is to the stellate C. tenuilobus, also from Mexico. This suggests two separate dispersal events from South America for the two Mexican species in the section. The replacement names C. longicolumellus and C. tenuicaulis are made for the later homonyms C. microcarpus and C. microstachys. Lectotypes are designated for C. andinus, C. angustifrons, C. burchellii, C. catinganus, C. cerino-dentatus, C. cerino-dentatus var. martii, C. cerino-dentatus var. warmingii, C. cuyabensis, C. eriocladoides, C. linearifolius, C. microcarpus, C. microstachys, and C. saxosus.