Truffles are hypogeous fungi which live in symbiosis with plant host roots in order to accomplish their life cycle. Some species, such as Tuber magnatum Pico, the 'white truffle', and Tuber melanosporum Vittad., the 'black truffle', are highly appreciated in many countries because of their special taste and smell. The great demand for the black and white truffles, the increasing attention towards other species of local interest for the rural economy (such as T. aestivum) together with a drop in productivity, have stimulated researchers to develop projects for a better understanding of the ecology of truffles by exploiting the new approaches of environmental microbiology and molecular ecology. Specific primers have been developed to identify many morphologically similar species, the distribution of T. magnatum has been followed in a selected truffle-ground, the phylogeography of T. melanosporum and T. magnatum has been traced, and the microorganisms associated with the truffles and their habitats have been identified.