Phylogenetic relationships in the genus Amanita were investigated using sequence data from the nuclear-encoded large subunit ribosomal DNA. Exemplar taxa were selected to represent the all sections from the current classifications of Singer, Bas and Jenkins. Phylogenetic analysis of the nuc-LSU region supports the taxonomic distinction of subgenera Amanita and Lepidella, as well as all nine sections previously recognized by Singer (R. Singer, 1986, The Agaricales in Modern Taxonomy, 4th ed.) including sections Amanita, Amidellae, Caesareae, Lepidella, Mappae, Phalloideae, Ovigerae, Vaginatae, Validae. Phylogenetic analyses among these nine terminal groups reveal several higher-level relationships which are also supported by morphological and biochemical characters. A phylogenetic classification is proposed which recognizes two subgenera (Amanita, Lepidella), four sections (Amanita, Vaginate, Phalloideae, Lepidella), seven subsections (Amanita, Ovigerae, Amidellae, Caesareae, Phalloideae, Vaginatae, Validae), and two series (Mappae, Validae).