Agapanthus africanus (L.), is a rhizomatous evergreen plant with fleshy roots, linear leaves, and umbellate inflorescence. It is native to southern Africa and commonly named the Nile lily or African lily. Regarding how closely related their morphologies are, the members of the genus Agapanthus have proven challenging to divide into distinct species. Additionally, no documentation was detected for the phytochemical screening, macro and micromorphology of A. africanus up to date. This inspired us to describe the macro and micromorphology of the flower, leaf, root, and rhizome of A. africanus and evaluate its phytoconstituents. This study demonstrated that A. africanus is free from any trichomes and is rich with various forms of calcium oxalate crystals, both these characteristics help to define the plant under investigation. Concomitantly, the fibrous layer of the anther, the papillosed stigma, and the ellipsoid, non-spiny pollen grains, were recorded in the morphology of the flower in this study. The phytochemical screening investigated the presence of saponins, phenolics, and flavonoids as the major constituents of the underground parts of A. africanus. As expected, this resulted in a more precise tool for taxonomical identification and species delimitation of the genus Agapanthus.