Basal stem rot (BSR) which affects many oil palm plantations in Malaysia is a destructive disease caused by the wood decaying fungi Ganoderma boninense. Information on response of oil palm to BSR is scarce, particularly concerning changes in the level of plant metabolites as the ultimate consequence of biological systems to genetic or environmental changes. A previous study on root inoculation technique was conducted by MPOB to identify oil palm progenies partially tolerant and susceptible to G. boninense infection that causes BSR. Therefore, in this study, parental palms of these progenies were identified and root tissues of both partially tolerant and susceptible parental palms of different BSR susceptibility were used to analyse metabolites by using a metabolomic-based approach. In this report, we examine the application of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to study aqueous methanolic extracts of root tissues of selected parental palms that are partially tolerant and susceptible to G. boninense. Collectively, 39 peaks were observed from LC-MS analysis operated in negative mode and of these, nine distinctive peaks were further characterised using accurate mass, isotopic pattern, database match and MS/MS experiment for compound identification. Together with several other metabolites, MS/ MS spectrum of procyanidin B was presented and all the major fragments were assigned with predicted sub-structures. The nine metabolites which were also successfully identified revealed a range of plant sugar and phenolics derivatives in parental palms root extracts. The novelty of the technique relies on the use of mass signals and the analytical strategy that are applicable to a wide range of analysis in oil palm root metabolomics. These findings provide information on the relationship between phenolic compounds as marker metabolites for disease detection and oil palm preventive mechanism against BSR.