The genus Fusconaia Simpson, 1900, as currently recognized, includes ~12 species in the tribe Pleurobemini. Two species are federally listed and several more are imperiled in part or all of their ranges; one species is probably extinct. However, classification at the species and genus level has been problematic, and it is unknown whether imperiled populations represent merely local ecophenotypic variations or endemic species. To provide additional evidence on the systematics of this group and to help establish conservation priorities, we sequenced two mitochondrial genes for all available species of Fusconaia as well as representatives of other genera of Pleurobemini and several outgroups. Both cox1 and nad1 provided well-resolved phytogenies. Some putative species show little molecular differentiation, supporting their synonymization. In particular, Fusconaia flava (Rafinesque, 1820), F. cerina (Conrad, 1838), and the easternmost populations previously assigned to F. askewi (Marsh, 1896) are not differentiated by our data. Although the majority of Fusconaia places in a well-supported clade that includes F. flava, the type species, others do not. “Fusconaia” barnesiana (Lea, 1838), the type of Pleuronaia Frierson, 1927, places with “Lexingtonia” dollabelloides (Lea, 1840) and “Pleurobema” gibberum (Lea, 1838). “Fusconaia” ebenus (Lea, 1831) and “F.” rotulata (Wright, 1899) form a distinct clade outside of Pleurobemini. “Fusconaia” succissa (Lea, 1852) is assigned to the pustulosa group of Quadrula (subgenus Rotundaria), along with Quincuncina infucata (Conrad, 1834). Conversely, the type species of Quincuncina, Quincuncina burkei Walker, 1922, is assigned to Fusconaia. Populations in the Ozark region assigned to F. flava and populations in the Suwannee River system assigned to Quincuncina infucata probably deserve species-level recognition.