Moringa is the sole genus in the family Moringaceae used for medicinal and nutrient purposes. Morphological features, phytochemical attributes, and molecular characterization were used for the genetic association and classification among Moringa oleifera, M. peregrina, and M. stenopetala. Moringa peregrina recorded a similarity of 84% lonely and placed M. stenopetala with M. oleifera into a cluster score with a similarity of 95.3%. M. peregrina is characterized by phenolic content (243 mg/100 g), flavonoids (7 mg/100 g), and antioxidant activity (1226.85 mg/100 g). GC-MS analysis revealed that M. oleifera contained twenty compounds with 2-decenal (E) (39.14%), 2-undecenal (15.51%), nonanal (3.60%), and 2-octenal, (E) (2.48%), while M. peregrina identified eighteen compounds with 2-decenal (Z) (25.42%), 2-docecen-1-al (9.35%), and 13-Docosenoic acid, methyl ester, (Z) (4.16%). M. stenopetala identified fifteen compounds containing 2-decenal (E) (26.67%), 2-undecenal (24.10%), and nonanal (4.40%). A broad sense of similarity has been scored between M. oleifera and M. stenopetala by the phytochemical compositions, especially the similarity in the main compounds such as 2-decenal (E), 2-undecenal, and nonanal. It can be concluded that efforts need to be expanded to pay attention to study Moringa taxa, due to the rarity of Moringa peregrina, and the focus should be on sustainable utilization and conservation. The potential of these taxa would greatly benefit indigenous species in terms of their maintenance, and there is a need for more comprehensive bio-prospecting studies. Therefore, this study evaluates the variability among Moringa and highlights the significance of leaf and seed ultrastructure to provide more information and evaluate potential approaches.