Oil palm industry in Malaysia is suffering from one major disease known as basal stem rot (BSR), caused by Ganoderma species. Microbes were isolated from soil samples collected from Crocker Range of Sabah and the percentage inhibition of radial growth (PIRG) against Ganoderma boninense was determined. There were 72 types of actinomycetes isolated from 20 soil samples and the most potential actinomycete (A19) showed the highest PIRG with 80.00%. The interaction of A19 with G. boninense was observed using scanning electron microscopy (SEM). G. boninense was inhibited by anti-fungal effect of A19 due to hyphae damage and A19 was successfully identified as Streptomyces spp. Metabolites of Streptomyces spp. A19, were extracted and ethyl acetate extract showed the highest inhibition to G. boninense. Minimum inhibitory concentration (MIC) of Streptomyces spp. A19 ethyl acetate extract was 0.18 mg ml-1. The extracts were then fractionated through solid phase extraction (SPE). SPE fractions (0.02 mg ml-1) showed better inhibition to G. boninense compared to crude extracts with the same concentration. Several antimicrobial compounds (ribostamycin, benzylmalic acid, landomycin B and salinomycin) were detected in these samples using Liquid chromatography-mass spectrometry (LC-MS). These metabolites may contribute to the antagonistic effect against G. boninense.