Forty years after the discovery of the helix nature of DNA and more than twenty after the first applications of recombinant DNA technology to the pharmaceutical industry, the Pandora's vase of biotechnology seems far from being empty. New products for agriculture and the food industry are constantly being placed on the market, and powerful monitoring techniques have been developed to track non-modified and genetically modified vaccines, viruses, microbes and plants released into the environment. Molecular approaches for taxonomic purposes, which might also be useful for quality control and assurance, have been successfully developed and used for taxonomic purposes in the last decade for both prokaryotic and eukaryotic cells, including yeasts and filamentous fungi. Mycorrhizae are one example of a traditional biotechnology that can greatly benefit from the latest molecular approaches. These universal symbioses between soil fungi and plant roots playa central role in most of the natural and agricultural ecosystems in such key processes as nutrient cycling, soil structural conservation and plant health. For these reasons, mycorrhizae have been successfully used to improve the quality of forest and agricultural seedlings, to produce high-quality micropropagated plants and to increase the production of edible mushrooms of high economic value, such as truffles. However, although controlled inoculation of oak and hazel seedlings with ectomycorrhizal truffles has been carried out for decades in France and Italy, and is still expanding commercially, several technological gaps remain to be filled.