White root rot (WRR) disease which is caused by Rigidoporus microporus is a major agricultural disease. The disease affects tropical fruits, forest trees, ornamental trees as well as rubber (Hevea brasiliensis) trees. Although WRR causes significant economic losses to planters, there is no effective method to control this disease. The understanding on the population genetics of R. microporus isolates could mitigate WRR disease in plant management. Therefore, the objective of this work was to elucidate molecular phylogeny of R. microporus isolated from rubber trees. Twenty seven R. microporus isolates were characterised using internal transcribed spacer (ITS), Beta-tubulin (β-tubulin) and translation elongation factor-α (tef1-α) sequences data. Phylogenetic tree analyses of R. microporus isolates were divided into two major groups; the Asian and African groups. However, there was no distinct geographical structuring in the Asian group, suggesting gene flow happened among the populations. Somatic Incompatibility (SI) test and Inter Simple Sequence Repeat (ISSR) marker revealed that the R. microporus in the rubber plantations partially clustered based on geographical regions. The genetic diversity of R. microporus by ISSR revealed four major groups. The findings of the present study provide a baseline data for breeders and plant pathologists to enable them strategise effective and sustainable WRR disease management.