Percina apina, the Tennessee Logperch, is described as a new species endemic to Tennessee and distributed in the Duck River system and Whiteoak Creek. The earliest collection records for Percina apina date to 1971 and the species was identified as Percina burtoni, the Blotchside Logperch. A phylogenetic analysis of mitochondrial DNA (mtDNA) published in 2006 showed that populations identified as Percina burtoni in the Duck River system and Whiteoak Creek were a new and undescribed species. In this study, we test the hypothesis that Percina burtoni is composed of multiple species through analyses of mtDNA, nuclear genetic variation, and traditional meristic trait morphology. Our analyses of morphological divergence, nuclear genotypes, mtDNA gene trees, and comparisons with other sister species pairs of logperches confirm the distinctiveness of Percina apina. Morphologically, Percina apina is distinguished from Percina burtoni through higher average numbers of lateral line scales (93.1 versus 89.9); pored lateral line scales (91.6 versus 88.8); rows of transverse scales (38.1 versus 33.6); and scales around the caudal peduncle (36.2 versus 33.5). The two species also differ in patterns of pigmentation; the lateral blotches in Percina apina are typically wider than high, whereas the blotches tend to be higher than wide in Percina burtoni. We recommend that future species descriptions of North American freshwater fishes leverage available genetic resources and include molecular phylogenetic assessments in analyses of taxon distinctiveness. In addition, we advocate the deposition of morphological data used in species descriptions to online data repositories to ensure that other researchers are able to evaluate and modify hypotheses of species delimitations.