Wood is an important economical resource for many tropical countries. Among the benefits of most of the tropical woody species, we can mention their natural durability and their capacity of withstanding outside environment without the use of chemical preservatives. Also, many of these tropical species show undeniable properties that people looked for such as aesthetic appearance and good mechanical property. Different marking systems are available in order to facilitate the traceability of wood but they present some limitations in their use at a larger scale. This study aims at developing a reliable technique to asses the geographical origin of different wood species. Wood can be colonized by destroying fungal microorganisms known as endophyte. The main objective of this work is to use these microorganisms as a molecular marker. An amplification of the ITS region has been done and used with CE-SSCP on tree different tropical species from 6 countries: Limba (Terminalia superba), Limbali (Gilbertiodendron dewerei-preussii) and Teak (Tectona grandis). Results show a grouping among different microbial profiles related to the wood species and discernment between Limba and Limbali. We show that microbial profiles could be used as a marker to ensure the proper origin of wood as part of an ecocertification for sustainable management of the forest. Also, they will help in controlling the itinerary of a wood product from forest to consumer.