The unionid tribe Pleurobemini is diverse but poorly-understood phylogenetically. Current classification recognizes two highly diverse genera, Elliptio Rafinesque, 1819 and Pleurobema Rafinesque, 1820, besides the moderately diverse Fusconaia Simpson, 1900, and several genera with one to three species. However, classification at the species and genus level has been problematic. Molecular data and re-examination of shell morphology and anatomy indicate new groupings of these taxa. Several genera proposed by early workers such as Rafinesque and Swainson are available, but are poorly-characterized and are often overlooked. We analyzed two mitochondrial genes, cox1 and nad1, for 50 species assigned to Pleurobemini, including the type species of each genus and as many other species as possible. Although the majority of studied species in Elliptio, Pleurobema, and Fusconaia show close affinities to the respective type species, the affinities of others are problematic. Genera or subgenera such as Eurynia Rafinesque, 1819, Sintoxia Rafinesque, 1820, and Pleuronaia Frierson, 1927, generally regarded as subjective synonyms, apply to some clades. Other clades or unaffiliated species have no available name. Quincuncina burkei (Walker, 1922), the type of the genus Quincuncina Ortmann, 1922, is assigned to Fusconaia Simpson, 1900. Fusconaia apalachicola (Williams and Fradkin, 1999), F. ebenus (Lea, 1831), F. rotulata (Wright, 1899) (also listed as Obovaria rotulata), F. succissa (Lea, 1852), Cyclonaias tuberculatus (Rafinesque, 1820), Uniomerus Conrad, 1853, and the Quincuncina infucata (Conrad, 1834) complex are all excluded from Pleurobemini. The first three are placed in the new genus Reginaia Campbell and Lydeard; Uniomerus Conrad, 1853 is assigned to Quadrulini; and the remainder belong in the pustulosa Lea, 1831 group of Quadrulini (genus Rotundaria Rafinesque, 1820).