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The genus Moringa (family Moringaceae), comprising 13 species distributed across Africa, the Indian subcontinent, and the Arabian Peninsula, represents a phytochemically rich and pharmacologically significant group of plants. Among these, Moringa oleifera, M. stenopetala, and M. peregrina have been most extensively investigated for their diverse array of bioactive compounds. This review presents a critical synthesis of specialized metabolites, including glucosinolates, flavonoids, phenolic acids, alkaloids, and isothiocyanates, with emphasis on their biosynthetic pathways, structural characteristics, and chemotaxonomic relevance. The pharmacological spectrum of these compounds is discussed in detail, covering antioxidant, anti-inflammatory, anticancer, neuroprotective, and antimicrobial activities, alongside mechanistic insights and molecular targets. Key research gaps are highlighted, particularly the underrepresentation of lesser-known Moringa species and the limited translational and in vivo validation of reported bioactivities. The review advocates for integrative methodologies such as metabolomics, transcriptomics, and bioassay-guided compound isolation to enhance species-specific characterization and therapeutic exploration. By consolidating current findings and proposing future research directions, this review aims to advance the scientific understanding of Moringa phytochemistry and pharmacology, and to facilitate the development of novel therapeutic agents from this underutilized genus.