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Eragrostis is a large genus in subfamily Chloridoideae of Poaceae. Recent phylogenetic analyses have suggested that the genus may not be monophyletic, that some of its segregate genera may be better placed within Eragrostis, and that current infrageneric classifications may not represent monophyletic groups. We have used molecular sequence data from the plastid locus rps16 and the nuclear gene waxy from a broad sample of Eragrostis species and representatives of six of the seven segregate genera to address these issues. We found that Eragrostis is monophyletic with the inclusion of several of the segregates, including Acamptoclados, Diandrochloa, and Neeragrostis. The placement of Cladoraphis and Stiburus is uncertain. Thellungia does not belong in Eragrostis and is actually more closely related to Sporobolus. These data also suggest that existing infrageneric classifications are inadequate and do not correspond to monophyletic groups within Eragrostis.