Quantitation of pathogenic Ganoderma species presence in oil palm plantation soil is crucial for basal stem rot (BSR) disease management where implemented disease control practices could be validated. Quantitative polymerase chain reaction (qPCR) has been widely applied in quantification of various pathogens in soil and plant tissues due to its high sensitivity. In this study, primers designed based on internal transcribed spacer (ITS) sequences were utilised for detection of pathogenic Ganoderma species. Its specificity and detection efficiency were tested using Ganoderma inoculated and non-inoculated soil samples. As for qPCR applications, primer IGbF-R was proven to be specific to Ganoderma boninense, and capable of amplifying its synonyms (G. orbiforme and G. miniatocinctum) in Ganoderma inoculated soil.