Ayahuasca is a traditional psychoactive beverage with pharmaceutical potential, prepared with Banisteriopsis caapi and Psychotria viridis, although the use of non-traditional plants - the so-called Ayahuasca analogues -, such as Banisteriopsis and related species, are also reported. These species are highly polymorphic and inconsistent in flowering periods, being difficult to identify when collecting to prepare the brew. To aid their separation in a vegetative state, some species used in Ayahuasca analogues (B. laevifolia, B. muricata and Diplopterys pubipetala) were characterized in their wood, outer bark and leaf morphoanatomy. We also verified whether their use is supported by histochemical data and investigated other compounds of pharmaceutical importance, in comparison with B. caapi. Usual techniques and methodology were used for histochemical and histological investigations, in addition to X-ray imaging for examining crystal organization and venation patterns. The wood anatomy descriptions of these species are given for the first time, and new characters were described, such as the tangential alignment of prismatic crystals in ray cells of D. pubipetala. Vegetative characters aid the species identification when reproductive material is unavailable, as the species differed in outer bark morphology, leaf morphology and anatomy and wood anatomy. Statistical analyses based on qualitative and quantitative anatomical features reinforce the recent distinction of Banisteriopsis and Diplopterys genera. Histochemical analyses revealed the presence of important compounds of potential pharmacological use: alkaloids, saponins, essential oils, lipids, pectin, tannins and general phenolic compounds, mostly in parenchymatous tissues in the bark and lesser in the wood. Alkaloids found mainly in the bark support the use of these plants in Ayahuasca analogues, although further studies are needed to ensure its safety and to exploit their pharmacological potential. It also raises an alternative extraction technique that could use solely strips of bark for small preparations of Ayahuasca, allowing for sustainable plant management.