Calathea, with an estimated 285 species, is the largest genus of Marantaceae and an important component of Neotropical herbaceous diversity. The genus is also of high importance for horticulture as species are cultivated for their showy, patterned leaves. Previous molecular phylogenetic studies indicated that the genus is polyphyletic, but have not provided a basis for redefining generic limits due to incomplete taxon sampling. To address this problem we analyzed DNA sequence data from three plastid markers (matK with flanking 3′ trnK intron, trnL intron and trnL-trnF intergenic spacer) and one nuclear marker (ITS) under a maximum parsimony criterion for a large and representative taxon sample covering all previously proposed infrageneric entities, and representing the full range of morphological variation known in the genus. Our results confirm that Calathea is polyphyletic. One clade, including subgenus Calathea, the C. lanicaulis group, and the genus Sanblasia, is sister to a clade formed by Ischnosiphon and Pleiostachya. The genus Monotagma is placed as sister to this clade. The remaining species form a second strongly supported clade as sister to a clade containing these other genera. Based on these findings Calathea is recircumscribed in a narrow sense and Sanblasia is placed in synonymy. The genus Goeppertia is resurrected and redefined to include all members of the second Calathea clade. Morphological characters defining each genus are provided. A total of 246 new combinations are made.