Foot rot disease of wheat is caused by the pathogens Fusarium cuImorum, F.avenaceum and Microdochium nivale. Symptoms of foot rot are a general browning of the stem base and leaf sheath. There is a discrepancy between the ability of fungicides to control these pathogens in vivo and in vitro, and no relationship between disease symptom severity and yield loss has been established in wheat. The identification of the causal agents of foot rot disease is not possible from examination of disease symptoms alone. This work showed that the azole fungicides flusilazole and prochloraz inhibited the germination of conidia and mycelial growth of F. culmonon, F. avenaceum and M. nivale in vitro to a varying extent. However, no consistent control of these pathogens in wheat was observed in the field using the same fungicides. Further studies employing a semicontrolled outdoor experiment showed a relationship between density and timing of inoculum application, disease symptom severity and yield loss in wheat artificially inoculated with F. culmorum and M. nivale. Molecular marker systems were used to address the problem of pathogen detection and identification. A Random Amplified Polymorphic DNA (RAPD) assay was developed to differentiate F.culmorum, F.avenaceum and two types of M.nivale (M.nivale var.nivale and M. nivale var .majus) in vitro. Selected RAPD products were cloned and sequenced and species specific primers constructed from this sequence infonnation. These primers were used in the polymerase chain reaction (peR) and were shown to detect the pathogens in host tissue. This technique was adapted by addition of a competitor fragment to the peR reaction resulting in a quantifiable competitive peR assay. Using this method the fungal biomass of each pathogen present in the host tissue could be estimated. The development of these techniques for the identification, detection and quantification of F. cuimorum, F.avenaceum, M.nivale var.nivale and M.nivale var.majus in plant tissue will allow more extensive studies of the epidemiology of these species, the competition between species and the effect of fungicides on these pathogens can be carried out.