Although phosphite has been effective in the control of P. cinnamomi in E. marginata (jarrah), the biochemical mechanisms behind phosphite protection are poorly understood. Using an aeroponics system, jarrah clones with moderate resistance to P. cinnamomi were treated with foliar applications of phosphite (0 and 5 g L−1). The roots were inoculated with zoospores of P. cinnamomi at 4 days before and 0, 2, 5, 8 and 14 days after phosphite treatment. Root segments were then analysed for activity of selected host defence enzymes (4-coumarate coenzyme A ligase [4-CL], cinnamyl alcohol dehydrogenase [CAD]) and the concentration of soluble phenolics and phosphite. Lesion development was most effectively reduced when phosphite concentrations within the roots were highest (i.e. days 8–14). During this time, the levels of host defence enzymes remained relatively unchanged. Lesion development was also effectively restricted when phosphite concentrations within the roots were lowest (i.e. days 2 and 5); a significant increase in host defence enzymes was associated with this decrease in lesion development. It was concluded from these studies that the effect of phosphite in controlling the pathogen is determined by the phosphite concentration at the host–pathogen interface. When phosphite concentrations within the roots are low, phosphite interacts with the pathogen at the site of ingress to stimulate host defence enzymes. At high phosphite concentrations, phosphite acts directly on the pathogen to inhibit its growth before it is able to establish an association with the host, and the host defences remain unchanged.