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Palaua, a genus of 15 species endemic to the fog-influenced lomas formations amidst the coastal deserts of Peru and Chile, is characterized by its unique irregularly arranged, superimposed carpels. The only exception to this character is P. sandemanii, which has carpels arranged in a single whorl, the state observed in the potential sister groups. To investigate the monophyly of Palaua and to compare previous infrageneric classifications in a phylogenetic framework, parsimony and Bayesian analyses were performed using plastid (psbA-trnH intergenic spacer) and nuclear (internal transcribed spacers 1 and 2) DNA sequences. There is evidence for three clades within a monophyletic Palaua: one comprising the two small-flowered species, P. inconspicua and P. modesta, as sister to the rest of the genus, a second uniting all species with dissected leaves, and a third containing the rest of the genus (species with entire to shallowly lobed leaves; except P. guentheri). In contrast to our expectations, P. sandemanii could not be confirmed as sister to the rest of the genus, but rather is nested within a monophyletic Palaua. Parsimony-based reconstruction of the evolution of carpel arrangement showed that there was a change in Malta from superimposed, irregularly arranged carpels to uniseriate carpels in P. sandemanii; however, Templeton and Shimodaira-Hasegawa tests did not reject the alternative hypothesis that the uniseriate carpels are ancestral. Besides carpel arrangement, leaf division (and not growth form) seems to be an appropriate character for infrageneric classification.