The tropane alkaloid scopolamine, an important precursor of active pharmaceutical ingredients due to its anticholinergic properties, can be extracted from leaf material of Duboisia R. Br., a member of the Solanaceae family. Robust and high-yielding Duboisia plants are a major requirement in cultivation because of challenges such as climatic changes and the rising demand of the active pharmaceutical ingredient. Therefore, breeding activities are carried out to improve Duboisia plants with regard to leaf and scopolamine yield maximization as well as a higher tolerance to environmental conditions. Molecular genetic analysis of highly conserved plastid sequences was used to prove the identity of the species Duboisia hopwoodii, D. myoporoides and D. leichhardtii. To evaluate different breeding options various flower characteristics have been analyzed by means of stereo microscopy for the three species. For D. hopwoodii and D. leichhardtii, all characteristics occur stably with nearly no variation. In contrast, the number of flower organs such as petals and anthers varied for D. myoporoides.