Phylogenetic analyses of morphological characters and plastid DNA sequences of rbcL and trnL-F are presented separately and combined for nine of the 12 genera of Themidaceae and seven genera of related Asparagales. The results from the combined analysis are the most highly resolved and provide strong support for the monophyly of Themidaceae. Within Themidaceae, the Brodiaea complex of western North America is weakly supported and the Milla complex of Mexico is moderately supported as monophyledc. Within the Brodiaea complex, there are three strongly supported novel clades: (1) Brodiaea and Dichelostemma, (2) Triteleia and Bloomeria, and (3) Muilla and Androstephium. Thus, the previously recognised Brodiaea sensu lato (Brodiaea, Dichelostemma and Triteleia) defined by the presence of an extended perianth tube is polyphyletic.