The classification and phylogenetic history of the Amaryllidaceae is reviewed since the dawn of molecular systematics in the 1990’s. The family is now recognized as comprising three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, of which the latter is the largest. The family likely had a Gondwanaland origin in what is now Africa. Agapanthoideae is monotypic, endemic to South Africa, and the first branch in the family tree of life; Allioidieae is sister to Amaryllidoideae. Four tribes are recognized in Allioideae: Allieae (monotypic, with nearly 1000 species of Allium across the Northern Hemisphere), Gilliesieae (5–7 genera in southern South America), Leucocoryneae (six genera mostly in southern South America), and Tulbaghieae (monotypic, with ca. 30 species endemic to South Africa). Amaryllidoideae is cosmopolitan, but mostly pantropical, consisting of 13 tribes. Centers of diversity occur in South Africa, South America and the Mediterranean region. The American clade is sister to the Eurasian clade (tribes Galantheae, Lycorideae, Narcisseae and Pancratieae) of the subfamily. The American Amaryllidoideae resolves as two monophyletic groups, 1) the hippeastroid clade (tribes Griffineae and Hippeastreae) and 2) the Andean tetraploid clade (tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae). Molecular analyses are reviewed for each main clade of the family, along with the resultant taxonomic changes. Directions for future studies are briefly discussed.