Ganoderma root rot disease has been reported world wide causing the death of affected hosts. The taxonomy of the genus Ganoderma is considered to be in disarray due to the use of basidiocarp morphological characters to differentiate the species which resulted in many synonyms, species complexes and possible misidentifications of species within the genus. The use of sexual compatibility tests and molecular techniques became powerful diagnostic tools to elucidate the taxonomy of Ganoderma species. Application of these techniques has resolved some of the taxonomic problems but the use of certain species names in the genus is still causing contention among taxonomists. The literature surrounding the taxonomy and techniques used in the taxonomy of the root rot fungus Ganoderma are considered in this thesis. It is clear that the taxonomy of Ganoderma is very difficult and it is still largely obscured by species complexes and incorrect species identifications. It is also evident that a single species concept will not aid in the identification of Ganoderma species. Rather, a combination of concepts based on morphology, mating tests and DNA sequence data should be used in elucidating the taxonomy of Ganoderma. Morphological characteristics as well as nucleotide sequence analysis of three gene regions; the internally transcribed spacer (ITS), the mitochondrial small subunit (mtSSU) and the intergenic spacer (IGS-1), were used to identify the causal agent of Ganoderma root rot of J. mimosifolia in the suburb of Brooklyn, Pretoria, South Africa. Morphological observations and DNA-based phylogenies revealed that all isolates collected from infected trees belong to a single species that reside in the G. lucidum sensu lato complex. Acacia mangium is a leguminous tree that is grown as an exotic plantation species in Indonesia. These economically important trees are threatened by Ganoderma root rot disease. This disease is considered to be the most important cause of losses in A. mangium plantations. Phylogenetic analysis of ITS sequence data showed that G. philippii is the primary agent of Ganoderma root rot in A. mangium in Sumatra, Indonesia.