The Leptostemonum clade of Solanum contains approximately 350–450 species, including the cultivated eggplant, S. melongena. This clade is characterized by the presence of prickles and apically attenuate anthers. Solanum section Androceras, the focus of this study, is a group of ca. 12 species belonging to the Leptostemonum clade. This section is unusual in the genus because of its mostly north temperate distribution and distinctive zygomorphic, heterantherous, and enantiostylous flowers. We infer phylogenetic relationships among 43 Solanum taxa, including 11 species and all varieties of sect. Androceras, using DNA sequence data from two nuclear regions (ITS and the granule-bound starch synthase gene [GBSSI or waxy]) and the chloroplast region trnT-F. The combined phylogenetic tree supports sect. Androceras as a monophyletic group sister to Solanum sect. Crinitum. Only one of the three series proposed by previous taxonomists, ser. Pacificum, is supported as monophyletic. Solanum tenuipes from the northern Chihuahua Desert is sister to the remaining species in sect. Androceras. Species-level relationships were also examined and it was found that two species, S. heterodoxum and S. citrullifolium, are not monophyletic. The ancestral flower color in sect. Androceras appears to be violet, with white and yellow flowers restricted to more derived clades. Characters formerly used to diagnose ser. Androceras, such as exclusively branched hairs and lack of complex foliar flavonoids, appear to have evolved more than once in the section.