Percina nebulosa and Percina bimaculata have been considered synonyms of P. caprodes for over 130 years. The taxonomic history of P. nebulosa is complicated by the fact that the name is preoccupied by Perca nebulosa Rafinesque. Percina bimaculata Haldeman is the available and appropriate name for this species, and the Chesapeake Logperch is the proposed common name. Recent phylogenetic analyses of mitochondrial DNA gene sequences support the hypothesis that P. bimaculata is a distinct species; however, a morphological comparison between P. bimaculata and other logperch darter species has never been published. An examination of morphological characters and a new molecular phylogeny of both mitochondrial and nuclear gene sequence data support the recognition of P. bimaculata as a distinct species most closely related to P. kathae and P. austroperca. Historically, P. bimaculata was distributed in the lower Susquehanna River Basin of Pennsylvania and Maryland and the middle to lower Potomac River Basin of Maryland, Virginia and the District of Columbia, USA. The species has not been recorded from the Potomac Basin since the 1930s and is currently found only in the lower Susquehanna River Basin. The restricted geographic distribution and extirpation from the Potomac Basin indicates that P. bimaculata is an imperiled species and may warrant protection under the Endangered Species Act of 1973. The molecular phylogeny also indicates that populations recognized as P. caprodes sampled from the upper Mississippi River Basin in Illinois, Wisconsin and Minnesota are not closely related to P. caprodes populations sampled from the Ohio, Tennessee, White and Hudson river drainages.