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The members of Amanita sect. Phalloideae (Fr.) Quel. are responsible for many fatalities worldwide. However, some species in this section have previously been reported as non-lethal and lacking deadly toxins. Sequences of five genes (ITS, nrLSU, RPB2, TEF1-alpha, TUB2) of species belonging to the section from tropical Africa, America, Asia, Australia, and Europe were included in this study to elucidate the phylogenetic relationships among the species. The results indicated that the lethal species are in one clade (subclade I) while the non-lethal species are divided into two clades (subclades II and III) within the section. Moreover, two non-lethal species from tropical Africa, namely A. ballerinoides and A. bulbulosa are newly described based on both morphology and molecular approaches. Phylogenetically, they cluster in the same subclade III with other known non-lethal amanitas, including A. ballerina, A. chuformis, A. franzii, A. levistriata, and A. pseudogemmata. Neither amatoxins nor phallotoxins were detected in A. ballerinoides and A. bulbulosa by LC-HRMS, which agrees with their placement in the non-lethal subclade III within A. sect. Phalloideae. Finally, a key to the West African species of Amanita sect. Phalloideae is provided.