This project has benefited from a Ph.D. fellowship of the Italian ISASUT (University of Torino) to Claude Murat. J. Díez is a receipt of a ‘Ramon y Cajal’ Researcher Contract from the Spanish ‘MCyT’. We thank Drs J-L. Jany (Laval University, Quebec) and A. Mello (University of Torino, Italy) for stimulating discussions, and Dr Rémy Petit (INRA-Pierroton) for discussion and running PERMUT on the current data. The provision of samples by M. L. Ballureau, C. Bazin, F. Beaucamp, P. Berthet, C. Beneteau, C. Bezombes, O. Bois, M. Bombled, I. Calvo, R. Chinouilh, A. Clare, A. Daniel, L. Danglade, J. P. Ducret, Mr Fayolle, B. Finot, H. Frochot, C. Galoger, A. Goyon, L. Genola, Mr Gillot, F. Gobeau, J. Goubier, A. Guillén, M. Honrubia, H. Huguet, G. Jallifier, Mr Junique, J. L. Lacam, A. Lauriac, Mr Lespinasse, J. Manreza, P. Materne, A. Meunier, M. Mondion, P. Moulin, S. Pallares, J. L. Prune, C. Raquillet, P. Rejou, J. F. Rey, R. Ribes, L. & G. Riousset, J. M. Rocchia, J. J. Roux, T. Sanchez, P. Sourzat, Y. Soulas, J. P. de Santis, P. Tabouret, A. Terrade, O. Viguier, J. Verbinski and L. Vergé is greatly appreciated. We also would like to thank all authors of freely available genetics software. We are grateful for the useful comments of the referees on an earlier version of the manuscript. This project was funded by grants from the Bureau des Ressources Génétique (research project BRG 69–68), the Institut Français de la Biodiversité (CNRS programme ‘Environnement, vie et sociétés’), INRA and the Italian Project ‘Tuber: Biotecnologia della micorrizazione’ funded by CNR.