Basal stem rot (BSR) caused by Ganoderma is the major disease of oil palm and therefore, of great economic importance to the Malaysian oil palm industry. Study of the biochemical interaction between Ganoderma boninense and the oil palm was carried out using a metabolomics-based approach. The aim of this study is to identify metabolites that are responsible for classification of different types of treatments that have been applied on the oil palm seedlings namely T1, inoculation with rubber wood block (RWB) fully colonised with G. boninense PER71; T2, inoculation with uncolonised RWB and T3, oil palm seedlings without inoculation of RWB. Spear leaves from oil palm seedlings were collected and analysed using liquid chromatography-mass spectrometry (LC-MS). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to distinguish components of interest and potential markers, which were identified by employing a mix of accurate mass, tandem MS (MS/MS) strategies with searches in spectral libraries. Chemometric results from oil palm spear leaf LC-MS data of 48-week after infection revealed asparagine and chelidonic acid abundance in T1 treated samples which was further confirmed using commercial chemical standard.