The pantropical genus Schefflera is represented by ca. 300 species in the American tropics, but due to limited sampling of the Neotropical species in previous phylogenetic studies of the genus, the monophyly of this group has remained tentative. To test this, an existing family-wide dataset of ITS and trnL—trnF sequences was expanded, and relationships were explored further by assembling new ITS and ETS datasets using a representative sampling from most of the morphological and geographical diversity of the group. These results were also used to test an informal, morphology-based classification of Neotropical Schefflera. Results of the phylogenetic analyses confirm the monophyly of Neotropical Schefflera, and its placement in the Asian Palmate clade of Araliaceae. Four clades were consistently recovered from all analyses, informally called the Calyptrate, Tremula, Jahnii, and Eastern South American clades, each of which corresponds closely to the previously recognized morphological groupings. The Eastern South American clade includes species from the Crepinella and Didymopanax groups, forming two geographically centered subclades (the Guayana Shield and Brazilian subclades, respectively). The composition of the Calyptrate clade overlaps considerably with the Neotropical elements of the Sciodaphyllum group, excluding S. tremula. That species, an Hispaniolan endemic, was instead sister to a Puerto Rican species from the Crepinella group (S. gleasonii), providing a third example of geographic structuring among Neotropical Schefflera species.