Phylogenetic relationships of 36 samples of Mannia and other Aytoniaceae were inferred based on sequences of the chloroplast trnL-trnF region and partial nuclear ribosomal LSU (or 26S) gene and using Targionia hypophylla and Athalamia hyalina as outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted on individual and combined molecular datasets. All phylogenetic tree topologies showed polytomies but suggest that Mannia has evolved from within Asterella and that there are two supported Mannia clades. Because Mannia is paraphyletic, with A. gracilis most closely related to M. triandra and M. pilosa, A. gracilis is transferred to Mannia. The major morphological differences between those genera are reevaluated. Based on molecular and morphological evidence Mannia is divided into the subgenera Mannia and Neesiella; Asterella subg. Graciles becomes a synonym of Mannia subg. Neesiella.