White clover (Trifolium repens L.) is an important component of low input pasture systems and can form effective associations with both nitrogen-fixing Rhizobium and phosphate-scavenging arbuscular mycorrhizal fungi (AMF). Understanding the genetic control of plant-AM interactions will allow clover breeders to develop genetic markers for selection of phenotypes favourable to AM symbiosis. Clover is normally an out-breeding species. Near-isogenic lines (NILs) developed from inbred lines of clover are ideal candidates for genetic studies since important agronomic traits are fixed. Four closely-related NILs provided plant material with contrasting phenotypes when inoculated with AMF Glomus mosseae. Seed-grown and clonal plants of these closely-related NILs were used to study gene expression associated with AM colonization and functioning. In order to relate plant phenotype responses specifically to changes in phosphorus availability, and ultimately to gene expression, a nutrient flowing culture system was developed in which nutrient application was constant and could be controlled. The only consistent phenotypic response discovered was a decrease in root production in response to AMF colonisation. Differential display demonstrated differences in gene expression in both leaves and roots of clover with and without AMF. These genes were mainly down-regulated in AMF plants and three were identified from a range of NILs under varying P concentrations. More apparent differences in gene expression were found in roots than in leaves, and in low rather than high AMF colonising lines. In total, 45 sequences were identified and cloned; 30 from leaves and 15 from roots. Sixteen sequences had homology with known genes, including protochlorophyllide oxido reductase and leghaemoglobin. The majority corresponded to ESTs from model legumes and from studies such as colonisation with AMF or Rhizobium, and phosphate or nitrogen starvation experiments. Six sequences were not found on any database, indicating that these corresponded to undiscovered genes either expressed or suppressed in AM white clover.