To date, there was no information available on the diversity and molecular characterization of fungi associated with oil palm decay. This study appeared as a response to that need for essential information on the overall, global biodiversity of fungi associated with oil palm decay. In this study, 5 isolates from 30 fresh samples from the Tanah- Gambus estates (infested fresh tissues and fruiting bodies) seemed to be Ganoderma boninense. In general, the strains isolated belonged to the class of the Ascomycetes and of the Mucorales. Some of these strains had a very fast growth rate (48h), making them highly invasive, such as the genera Trichoderma or Fusarium. The PDA-Chloramphenicol medium seemed to be the most appropriate. Adaptation of the protocol developed in this study enabled us to extract DNA from all our samples using just 40 mg of mycelium of Ganoderma fruiting bodies and of fresh oil palm tissues. To date, the sequencing result for 250 samples gives a single species name and very high BLAST performance criteria (evalue, % coverage) for the best 10 results. After BLAST, we obtained 17% the genus Ganoderma, 41% of Ascomycetes, yeasts and other Basidiomycetes, 17% miscellaneous (plants etc.) and 25% of unusable sequences. An initial analysis of the interspecific phylogenetic relations of Ganoderma, based on a comparison of rDNA sequences, 5.8S and ITS 2, revealed clearly distinct clades where the species tended to group according to the nature of the sample and the geographical origin, particularly the species from Benin and Indonesia, and the freeze-dried samples from Indonesia.