Ganoderma boninense is a fungus which causes basal stem rot disease in oil palm and affects the palm oil productivity. Fungal attack on oil palm results in numerous host-specific biochemical responses. The activation of some of them is critical for the oil palm’s survival. The oil palm may releases some compounds which may act as a defence mechanism during the fungal attack. Many efforts have been made to control the basal stem rot disease spread. However, the infected palm did not show any early symptoms, which aggravates the control measure action as early as possible. Biochemical study via gel-based proteomic was conducted to identify the differentially expressed proteins during artificial infection of Ganoderma boninense on oil palm at day 7. Control palms were also prepared to get rid of background effect. The oil palm was subjected to two different treatments (infected and control). Artificial infection was conducted via root-inoculation technique, which the primary root was inserted into a rubber wood block filled with Ganoderma inoculum. The respected roots were taken for phenol-based protein extraction method (Sheffield et al., 2006). Proteome maps with different molecular masses and pH, ranged between 10 to 100 kDa and 3 to 11 respectively, were successfully dissolved. In total, 450 protein spots per gel were emerged and only 25 protein spots were determined as highly expressed in the infected root at day 7. MALDI-TOF MS analysis was carried out and the mass spectra were searched against in-house database. About 12 protein spots with significant MOWSE score was also searched through other databases (NCBI, Swiss Protein, InterProScan, Pfam, TAIR) for confirmation. These spots gave high identities to proteins that involved during fungal infection in other plants.