Percina brucethompsoni, the Ouachita Darter, is described as a new species endemic to the Ouachita River system in the Ouachita Highlands of Arkansas. Bruce Thompson first noted the distinctiveness of the new species from the nominal P. nasuta distributed in the White River and Arkansas River basins in his 1977 doctoral dissertation. The new species is delimited through morphological comparisons with P. nasuta and a phylogenetic analysis of the Percina subclade Swainia using two mitochondrial genes. More than 385 specimens were examined for the morphological comparisons, and 54 specimens were sampled for mitochondrial DNA sequencing. Percina brucethompsoni is distinguished from P. nasuta by a shorter snout, a broader and deeper head, six versus seven branchiostegal rays and specific patterns of lateral pigmentation on the side of the body. Phylogenetic analysis of DNA sequences sampled from two regions of the mitochondrial genome indicate that P. brucethompsoni is the sister species of P. nasuta populations in the White River drainage. Neither P. nasuta nor P. phoxocephala are monophyletic in the mitochondrial DNA gene tree. Specimens of P. phoxocephala from the Red River drainage are resolved as the sister lineage of a clade containing all other sampled populations of P. phoxocephala, P. brucethompsoni and P. nasuta. Percina nasuta and P. phoxocephala sampled from the Arkansas River drainage form a clade that is the sister lineage of a clade containing P. brucethompsoni and P. nasuta from the White River drainage.