Fluorescent compounds have been reported in plant leaves, having an important biological role in the protection towards UV irradiation. It is also known that stress conditions in plants stimulate the production of some of these compounds in their aerial portion. However, less is known about their production by roots or seeds and their presence in the soil surrounding them. We report here that, soybean, sunflowers and rapeseed produced fluorescent seed and root exudates. Phosphorus deficiency in rapeseed stimulates the excretion of fluorescent compounds by roots, mainly chlorogenic acid and scopoletin. When the effect of the fluorescent fraction from soybean seed exudates on Macrophomina phaseolina was tested, an enhanced induction of sclerotia formation, hyphal squeezing and lysis in the mycelium was observed. The fluorescent compounds and perhaps other chemical molecules also present in exudates might constitute a transitory defense barrier against early attack by pathogens.