An overview of truffles (now considered to belong in the Pezizales, but formerly treated in the Tuberales) is presented, including a discussion on morphological and biological traits characterizing this form group. Accepted genera are listed and discussed according to a system based on molecular results combined with morphological characters. Phylogenetic analyses of LSU rDNA sequences from 55 hypogeous and 139 epigeous taxa of Pezizales were performed to examine their relationships. Parsimony, ML, and Bayesian analyses of these sequences indicate that the truffles studied represent at least 15 independent lineages within the Pezizales. Sequences from hypogeous representatives referred to the following families and genera were analysed: Discinaceae-Morchellaceae (Fischerula, Hydnotrya, Leucangium), Helvellaceae (Balsamia and Barssia), Pezizaceae (Amylascus, Cazia, Eremiomyces, Hydnotryopsis, Kaliharituber, Mattirolomyces, Pachyphloeus, Peziza, Ruhlandiella, Stephensia, Terfezia, and Tirmania), Pyronemataceae (Genea, Geopora, Paurocotylis, and Stephensia) and Tuberaceae (Choiromyces, Dingleya, Labyrinthomyces, Reddellomyces, and Tuber). The different types of hypogeous ascomata were found within most major evolutionary lines often nesting close to apothecial species. Although the Pezizaceae traditionally have been defined mainly on the presence of amyloid reactions of the ascus wall several truffles appear to have lost this character. The value of the number of nuclei in mature ascospores as a delimiting family character is evaluated and found to be more variable than generally assumed.