Moringa species are important multi-purpose tropical crops, as human foods and for medicine and oil production. There has been no previous comprehensive analysis of the secondary metabolites in Moringa species. Tissues of M. oleifera from a wide variety of sources and M. stenopetala from a single source were analyzed for glucosinolates and phenolics (flavonoids, anthocyanins, proanthocyanidins, and cinnamates). M. oleifera and M. stenopetala seeds only contained 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate at high concentrations. Roots of M. oleifera and M. stenopetala had high concentrations of both 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate and benzyl glucosinolate. Leaves from both species contained 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate and three monoacetyl isomers of this glucosinolate. Only 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate was detected in M. oleifera bark tissue. M. oleifera leaves contained quercetin-3-O-glucoside and quercetin-3-O-(6' '-malonyl-glucoside), and lower amounts of kaempferol-3-O-glucoside and kaempferol-3-O-(6' '-malonyl-glucoside). M. oleifera leaves also contained 3-caffeoylquinic acid and 5-caffeoylquinic acid. Leaves of M. stenopetala contained quercetin 3-O-rhamnoglucoside (rutin) and 5-caffeoylquinic acid. Neither proanthocyanidins nor anthocyanins were detected in any of the tissues of either species.