ABSTRACT Mango wilt, caused by Ceratocystis fimbriata, is one of the most important diseases affecting mango yields in Brazil. Information regarding the biochemical mechanisms involved in mango resistance against C. fimbriata is absent in the literature. Thus, the present study determined and quantified alkaloids and phenolics in the stem tissue of mango plants from Palmer (susceptible) and Ubá (resistant) cultivars. Furthermore, it was examined the effect of these secondary metabolites against C. fimbriata growth in vitro. The high-performance liquid chromatography revealed that the concentration of two alkaloids (theobromine and 7-methylxanthine) and six phenolic compounds (caffeic acid, p-coumaric acid, gallic acid, protocatechuic acid, catechin and epicatechin) in the inoculated plants from cv. Ubá was higher in comparison with inoculated plants from cv. Palmer. The concentration of the secondary metabolites was higher in the non-inoculated plants from cv. Palmer than in the inoculated ones, while the opposite was observed for plants of cv. Ubá. Peaks in the concentrations of secondary metabolites in the inoculated plants from both cultivars occurred at 7 and 14 days after inoculation. The different concentrations (10 to 30 mg∙mL−1) of secondary metabolites added to the Petri dishes greatly inhibited C. fimbriata growth over time. These results suggest that secondary metabolites played an important role in the resistance of mango plants against C. fimbriata infection.