The phylogenetic relationships of Croton section Cyclostigma sensu Webster were examined using nuclear ribosomal ITS and plastid spacer trnL-F sequences from 48 of the 63 species in the group, including members of the four recognized subsections and representing the group's full morphological and geographic range. The two gene phylogenies concurred that section Cyclostigma sensu Webster is polyphyletic, with its members appearing in nine different clades throughout Croton. The clade that retains the taxonomic type of the section and about half of the species sampled is redefined here as a reduced, monophyletic section Cyclostigma, and the remaining species are placed in other sections or informal clades. The ITS and chloroplast phylogenies are discordant regarding the position of the redefined section Cyclostigma suggesting that reticulate evolution might have played a role in the evolutionary history of this group. These results highlight that the tree habit has evolved on multiple occasions in Croton, and that there are other morphological characters that can effectively distinguish different tree lineages in the genus.