Protocols for isolating and amplifying fungal DNA from ectomycorrhizae, overcoming the presence of PCR inhibitors, were established to ensure a fast and reliable truffle mycorrhizal identification. By using species-specific ITS primers in multiplex PCR, morphologically very similar Tuber melanosporum, Tuber indicum and Tuber brumale ectomycorrhizae were identified in a single step of amplification, irrespective of their physiological stage. The molecular method assures a more accurate and reliable monitoring of nursery-inoculated plants both before and after their in-field planting, than any morphological or ITS/ RFLP analyses so far performed. It should also prevent frauds, already a problem, and the potential for environmental damage due to the incorrect typing of the allochthonous species T. indicum as European truffle species, when the identity of ectomycorrhizae is based solely on morphology
