Phenylpropanoid pathway enzymes are involved in plant defence pathways leading to lignification, synthesis of secondary metabolites, such as salicylic acid and phytoalexins, wound healing and the oxidative burst. Endophytic non-pathogenic Fusarium oxysporum isolate V5w2 has been reported to show antagonistic effects against Radopholus similis in the screenhouse. An experiment was designed to study root biochemical changes (PAL, POX and PPO activities) and R. similis numbers in susceptible and tolerant bananas following inoculation with isolate V5w2. Constitutive expression of PAL and PPO were similar between the susceptible and tolerant cultivars, while constitutive POX activity was higher in the tolerant cultivar. PAL activity was suppressed in both cultivars 7 days after endophyte inoculation (7 dai), but was significantly up-regulated in the susceptible cv. Nabusa at 30 days post nematode challenge (dpnc) in endophyte-inoculated plants. In the tolerant cultivar, PAL activity was up-regulated in R. similis-challenged plants at 7 and 30 dpnc, irrespective of endophyte inoculation. POX and PPO were transiently up-regulated in cv. Nabusa 7 dai, exceeding levels observed in non-inoculated plants of the same cultivar. POX activity was up-regulated at 7 dpnc in endophyte-inoculated cv. Nabusa plants challenged with R. similis. In the tolerant cultivar, POX and PPO activities were similarly up-regulated in R. similis-challenged plants at 7 dpnc, irrespective of endophyte inoculation. The findings of this study implicate PAL, POX and PPO in banana defence against the root-burrowing nematode R. similis. Our findings further demonstrate the ability of endophytic F. oxysporum isolate V5w2 directly to induce POX and prime PAL in the susceptible cv. Nabusa for greater up-regulation following R. similis challenge.