Traceability is defined according to ISO 9000 as the ability to retrieve the origin and use of an article or an activity through a registered method. Its implementation in the timber industry is delayed because of limits of classical identification systems with regard to the nature of timber and features of the manufacturing process. One hypothesis of tracing the source of timber and its products is by analysing in a global way the microbial communities of timber and linking this analysis statistically to its geographical origin. We proposed a very innovative tool of fungi ecology, the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), that was used to characterise the fungi flora of two tropical timbers species, teak and limbali from four countries: Côte d'Ivoire, Cameroon, Central African Republic and French Polynesia. The aim was to show if there was statistical relation between the fungal communities of the timbers and their geographical origins. PCR-DGGE method is a new, simple and cheap traceability tool that can trace the original locations of timbers.