Malesherbiaceae are an angiosperm family allied with Turneraceae and Passifloraceae. The family contains 24 species in the single genus, Malesherbia, and is distributed in the arid Andes and coastal deserts of Chile, Peru, and Argentina. Although there are several morphologically cohesive groups of species in the genus, no subgenera or sections have been recognized. A phylogeny for the family was reconstructed from ITS sequence data using parsimony, implied weights, successive approximations, and maximum likelihood analyses. Parsimony, implied weights, and successive approximations yielded almost identical topologies having four strongly supported clades and one weakly supported clade. Maximum likelihood analysis using model TrNef G resulted in a topology showing the same four well supported clades, but the root moved to break the monophyly of the fifth clade. The four well-supported clades each contain morphologically similar species, and the fifth clade also shows some morphological cohesion. The five clades are morphologically divergent and may be recognized taxonomically at the level of section. Five sections, Albitomenta, Cyanpetala, Malesherbia, Parvistella, and Xeromontana, are described. A key to the sections is provided.