Gossypol and related terpenoid compounds play an important role in defense against microbial pathogens and insect pests in cotton. Previously, we have identified and cloned an enzyme, desoxyhemigossypol-6-O-methyltransferase (dHG-6-OMT), that is responsible for converting non-methylated form of these compounds into methylated form, which are less toxic to plant insect pests and pathogens than the non-methylated counterparts. Blocking this enzyme by RNAi resulted in more than 90% reduction of methylated terpenoid compounds, but the amount of the non-methylated compounds remained almost unchanged in the roots of RNAi plants compared to that of the wild type siblings. The effect of these altered defense compounds profile in the RNAi plants on disease resistance was assessed by inoculating plants with a Fusarium wilt pathogen Fov1 in the presence of root-knot nematodes. The RNAi plants showed slightly greater reductions in shoot weight and root weight than the wild type sibling plants 5 weeks after inoculation. Thus, the methylated terpenoid compounds, though less toxic than the non-methylated counterparts, also contribute to disease resistance in cotton.