For the protection of soils against erosion and groundwater against leached-out substances considerable progress has been achieved by growing a row crop like maize together with green manure species. Within such systems the interactions between the plant species need to be sufficiently managed; a knowledge base must be established on the exploration of the available soil volume by roots in space and time, an almost unsolvable methodological problem up to now. We have been successfully calibrating an innovative methodology that is based on root fluorescence of genetically transformed maize (Zea mays L.); it expresses the green fluorescent protein (GFP), which can be observed through minirhizotrons at defined soil positions with a special camera. By this unique methodology we are finally able to precisely describe the morphological processes of cohabitation in the root zone. The combination of this precise information about the root systems with data on shoot growth will provide a unique and integrated analysis of soil, root and shoot processes. Root fluorescence is a powerful and urgently needed tool to understand root physiology and ecology and offers new opportunities for research in intercropping, agroforestry and weed science.