Root rot caused by Ganoderma spp. is a serious concern in commercial plantations of Acacia mangium in Indonesia. This study surveyed root rot incidence and spatial arrangement in commercial plantations and trials. In second rotation commercial plantations in Sumatra and Kalimantan, root rot incidence was recorded between 3 and 28% in trees aged from three to five years old. The compartments surveyed in Riau province and East Kalimantan had significantly higher root rot than South Sumatra. In a progeny trial of A. mangium in Java, root rot incidence was surveyed twice, when trees were eight and again at nine years old. Root rot incidence was about 7 and 13% respectively. Spatial analysis by distance indices (SADIE) revealed that infected trees were randomly distributed at the first time point but tended to become aggregated by the time of the second survey. This highlights the probability of vegetative spread of the fungus after initial introduction to the site. Assessment of root rot incidence on the basis of A. mangium provenance did not reveal any statistically significant differences.