The effect of 6-benzylaminopurine on polymethoxyflavone levels in tangelo Nova fruits and the possible participation of these secondary metabolites in defense mechanisms against Phytophthora citrophthora are studied. The in vitro study of the inhibitory effect of these compounds on fungal growth reveals that nobiletin is the most active agent followed by sinensetin, heptamethoxyflavone, and tangeretin. Treatment with 100 ppm of 6-benzylaminopurine increased the levels of these polymethoxyflavones in this Citrus hybrid and also enhanced the in vivo resistance of the fruit to the fungus by approximately 60%.