Late wilt, a severe vascular disease of maize caused by the fungus Harpophora maydis, is characterized by relatively rapid wilting of maize plants, before tasseling and until shortly before maturity. In Israel, the disease becomes a major problem in recent years. The pathogen currently controlled using varieties of maize has reduced sensitivity. In earlier work, we modified a molecular method for use as a diagnostic tool to evaluate the disease progress in field infested plants. Several fungicides suppressed H. maydis in vitro and in a detached root pathogenicity assay. Seedling pathogenicity assay enables us to identified H. maydis DNA in the host root and stem tissues 18 days after sowing in both susceptible and tolerant maize plants. Although the infested plants exhibited no wilt symptoms, their roots were significantly shorter in length. This seedling assay was used to demonstrate the suppressive effect of the fungicide Flutriafol on H. maydis virulence. The method of assaying the pathogen in a series of trials starting in a plate assay, followed by a detached root and resulting in a seedlings pathogenicity assay, using molecular and morphological approaches could be generalized to other plant pathogens.