This study provides a preliminary phylogeny of the Celtis species from the neotropical region with emphasis on the South American species. We analyzed 19 taxa using the plastid psbA-trnH and nuclear ITS 4-5, and FA16180b markers. The sequence data were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. The South American species were highly supported as monophyletic, while the North American species were recovered as paraphyletic. The endocarp morphology corroborated the lineages within the molecular phylogeny and helps to differentiate the species, to recognize a new species Celtis serratissima, and to reestablish two previously known species, Celtis clausseniana (Wedd.) Miq. and Celtis spinosissima (Wedd.) Miq. These three species emerged among one of the three lineages of the tropical South American species. Celtis serratissima is thus described, illustrated, and compared to its most closely related species.