Oil palm (Elaeis guineensis Jacq.) is an oil crop widely cultivated throughout South-east Asia countries. Unfortunately, the industry is badly affected by Basal Stem Rot (BSR) disease, caused by soil-borne pathogen, Ganoderma boninense, which is the most devastating and widespread disease in oil palm. Although some investigations have been conducted, complete understanding on BSR infection is yet to be achieved. In this article, observation on roots of inoculated oil palm seedlings under scanning electron microscopy showed G. boninense colonisation predominantly formed on root surface, proving endophytic colonisation primarily through the hair base, crossing epidermal cells, and followed by spreading into cortical cells which a possible pathway leading to vascular system. It also showed the formation of highly dense hypal network within the colonised area, mainly in the epidermal and cortical cells. By six months of inoculation, cell compartment of infected roots was lost and noticeable changes in the root cells structure were observed. The present study provides additional insights in the infection process and pathogen route inside the host tissue and may be useful for development of disease control strategies.