Host resistance is the most effective and practical control method for the management of Verticillium wilt in olive caused by Verticillium dahliae, which remains as one of the major current threats to this crop. Regrettably, most olive cultivars of agronomic and commercial interest are susceptible to V. dahliae. We previously demonstrated that wild olive (Olea europaea L. subsp. europaea var. sylvestris) clone AC18 harbours resistance to the highly virulent defoliating (D) V. dahliae pathotype, which may be valuable as rootstock and for breeding new, resistant olive cultivars. Mechanisms underlying disease resistance may be of constitutive or induced nature. In this work we aim to unravel constitutive defences that may be involved in AC18 resistance, by comparing the transcriptome from uninfected stems, of AC18 with that of the highly susceptible wild olive clone AC15, GO-term enrichment analysis revealed terms related to systemic acquired resistance, plant cell wall biogenesis and assembly, and phenylpropanoid and lignin metabolism. qRT-PCR analysis of phenylpropanoid and lignin metabolism-related genes showed differences in their expression between the two wild olive clones. Phenolic content of stem cell walls was higher in the resistant AC18. The total lignin content was similar in resistant and susceptible clones, but they differed in monolignol composition. Results from this work identifies putative key genes in wild olive that could aid in breeding olive cultivars resistant, to D. V. dahliae. The research highlights the constitutive defence mechanisms that are effective in protecting against pathogens and our findings may contribute to the deciphering the molecular basis of VW resistance in olive and the conservation and utilization of wild olive genetic resources to tackle future agricultural challenges towards.