Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV) is a major damaging disease of cotton. Chemical control is currently ineffective and has led to resistance of the pathogen. In addition, pesticides are indexed for their negative impact on the environment and on human health. The objective of this study was to evaluate the impact of sugarcane stem residue filtrate (FCS) and cotton stem residue filtrate (FTC) residue filtrate on FOV causal agent of the disease. These two polysaccharide biocontrols allowed a good accumulation of gallic acid, caffeoyl D-glucose, catechin, gossypetin and 3-p-coumaroylquinic acid and the de novo synthesis of epicatechin, protocatechic acid, ferulic acid, trans-resveratrol, trans-piceide, pterosilbene, 5-caffeylquinic acid, rutin, astringin and isoquercetin. However, 5-caffeylquinic acid and rutin are specific to FCS while astringin and isoquercetin are specific only to FTC. This difference in polyphenol synthesis caused 1% mortality in FTC and 8% in FCS. This indicates that astringin and isoquercetin are phenolic markers of resistance to FOV followed by 5-caffeylquinic acid and rutin. FTC can be used as a preventive control of Fusarium wilt in cotton.