The phylogenetic relationships among members of the Neotropical clade of Miliuseae were inferred using Bayesian inference, maximum likelihood, and parsimony on a dataset of six plastid regions (ndhF, matK, psbA-trnH, rbcL, rps16-trnQ, and trnL-F). The phylogenetic hypothesis obtained indicate that the Neotropical clade of Miliuseae is a monophyletic group, composed of two distinct lineages: the first comprises the genera Sapranthus and Tridimeris, and the second is composed of Desmopsis, Stenanona, and two potentially new taxa, which together form the Desmopsis-Stenanona clade. However, the relationships within the Desmopsis-Stenanona clade are not fully resolved; the phylogenetic results indicate that Desmopsis and Stenanona, as currently circumscribed, are not monophyletic. The morphological characteristics that distinguish each genus and potential synapomorphies are discussed. We conclude that the observed variation in floral and fruit characteristics among the members of the Desmopsis-Stenanona clade could be driven by interactions with their main pollinators and fruit dispersers. Based on these results we propose that the Neotropical clade of Miliuseae needs to be recognized at the subtribe level, under the name of Sapranthinae.