Phylogenetic analyses were performed based on four plastid DNA sequences to determine if the Daturae and Datura are monophyletic and to understand their relationships and classification. Species of Datura have been divided into three sections based upon the position and type of the fruit: Ceratocaulis, Datura, and Dutra. Our analyses confirmed the monophyly of the Daturae clade with two genera, Datura with herbaceous species and Brugmansia with woody species. The Datura clade consists of two distinct lineages, that of D. ceratocaula, corresponding to the monospecific section Ceratocaulis, and one that gives rise to the remaining species of the genus. The large clade readily divides into two groups but they do not correspond to the conventional classification of the genus. Species with regularly dehiscent capsular fruits are present in both groups while species with irregularly dehiscent capsules are found in only one group. Because section Dutra is polyphyletic, realignment of species within two traditional sections is necessary as follows: Datura containing D. arenicola, D. discolor, D. ferox, D. quercifolia, D. kymatocarpa, D. leichhardtii, and D. stramonium; Dutra containing D. inoxia, D. lanosa, D. metel, D. reburra, and D. wrightii. The seed margin clearly distinguishes these sections, rather than the combination of fruit position and dehiscence which has been used previously.