A pathogen-selective fungicide trial was established at a site with a history of continuous maize cultivation with stubble retention to assess the impacts of Pythium, Fusarium and Rhizoctonia root diseases on maize productivity. High soilborne populations of Pythium and Fusarium were detected at sowing, with no significant differences in their distributions across the site. Significant increases in Fusarium and Pythium isolates were recovered from maize rhizosphere soils after the first 12 weeks of crop growth. While no isolates of phytopathogenic Rhizoctonia were recovered from soil or maize roots, 63 and 100% of roots examined were colonised by Pythium and Fusarium spp., respectively. Fungicides were, therefore, ineffective in suppressing rhizosphere fungal populations and inhibiting root infection and disease development. As a result, there were no significant increases in crop establishment, early crop growth (biomass) or grain yields with any of the pathogen-selective treatments. DNA sequencing identified six Pythium and five Fusarium spp. from infected maize roots (internal transcribed spacer 5.8s rDNA) and rhizosphere soils (rDNA and translation elongation factor-1α). These species have previously been reported as saprophytes on crop residues and as components of a root-disease complex contributing to seedling damping-off and root and stem rots of maize. Growth responses of rotation crops grown in natural and sterilised continuous maize soil indicated that soilborne root pathogens significantly reduced biomass production of maize and wheat, but not Adzuki bean and canola. Fungal isolation frequencies from these crops implied host-mediated selection of Pythium but not Fusarium spp., the former showing a preference for and greater pathogenicity towards maize and wheat.