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Basal and upper stem rot of oil palm is caused by the agaricomycete Ganoderma boninense. This study investigated the transmission of basal stem rot from Ganoderma‐infected oil palm stumps to young oil palm seedlings. Low seedling mortalities (2.5%) were observed in a field trial after 24 months, but G. boninense could be detected in the rachis, bole and roots of a significant proportion of seedlings that were outwardly healthy. A high level of genetic heterogeneity amongst G. boninense isolates within the trial area was revealed. Furthermore, germinated seedlings growing in close proximity to infected palms in a mature oil palm field contained multiple isolates of G. boninense indicating that colonization of roots by basidiospores and dikaryons, arising from mating between basidiospores, is a common occurrence in oil palm plantations. The probability that basidiospores are a direct source of inoculum in addition to diseased trunk tissue is discussed as a means of explaining the observed heterogeneity in populations of G. boninense on oil palm. Such a scenario presents challenges for the long‐term management of basal stem rot. [ABSTRACT FROM AUTHOR]