Phylogenetic analysis of DNA sequences from chloroplast regions and nuclear ribosomal ITS was conducted to test the monophyly of Cestrum sect. Habrothamnus and investigate its relationships with other sections of Cestrum. Molecular divergence was very low among the sampled species, suggesting a rapid diversification in Cestrum. Individual and combined analyses of these molecular data sets using maximum parsimony and Bayesian inference reject the monophyly of the traditionally recognized sections of Cestrum, including sect. Habrothamnus. Infrageneric classifications will require significant revision. Nevertheless, the resolved monophyletic clades in this molecular analysis are geographically structured.