The trend in glasshouse horticulture has always been to keep culture systems as clean as possible by using new substrates, by applying disinfection techniques, pathogen-free propagation material, etc. However, several root diseases cause problems under these conditions. Especially, zoospore-producing organisms such as Pythium and Phytophthora spp. are well adapted to aquatic life and flourish in soilless substrates. The present paper shows the importance of the microflora in suppressing root pathogens in soilless systems, either by introducing selected antagonists or by stimulation of a beneficial microflora. The limited volume of substrate and a 'biological vacuum' in soilless systems, facilitate inoculation and establishment of antagonists. Examples of soilless systems that contain a suppressive microflora are described. Moreover, the impact of recirculation and disinfection of the nutrient solution on pathogen spread and disease suppression is discussed. Increased knowledge on the beneficial microflora, its ecology, and treatments that influence its composition, will stimulate the exploitation of microbially balanced and optimised soilless systems.