Considering the morphological similarities, taxonomic complexity of the genus Cynophalla of the family Capparaceae A. Juss. an the medicinal use of its species and its potential as green energy, this study aimed to compare potential morphoanatomical diagnostic characters of the species Cynophalla flexuosa and Cynophalla hastata to determine authenticity parameters. Furthermore, it aimed to perform a histochemical study of the leaf blades due to their medicinal use. The morphological analysis was carried out using different characters, such as phyllotaxis, shape, among others. For microscopic analyzes semi-permanent slides were prepared containing cross-sections of the stems, petioles and leaf blades. We also prepared paradermal sections of the leaf blades. The analyses were carried out using light microscopy. For the histochemical analysis, we used different reagents according to the target metabolite and analyzed them using light microscopy. Phytochemical tests of the methanolic extracts of the leaves were performed using Thin Layer Chromatography. C. flexuosa has erect branches, elliptical to obtuse leaves with an obtuse to acute apex and obtuse base, globose flower buds, and fruit in a follicular, torulous capsule shape. C. hastata has gently curved branches, oblong-elliptical leaves with a rounded apex and obtuse base, corymb axillary inflorescences with quadrangular flower buds, and cylindrical foliolate capsular fruit. The anatomical characterization showed the characters of general occurrence in the Capparaceae family and those that allow the differentiation of C. flexuosa and C. hastata. The histochemical and phytochemical characterization revealed the sites of synthesis and/or storage of metabolites. Thus, the results presented comparative data on the anatomical characters and histochemical and phytochemical characterization of the species, thus increasing the taxonomic knowledge of the genus Cynophalla and contributing data for future in-depth studies on the species’ potential as renewable energy.