Percina freemanorum, the Etowah Bridled Darter, is described as a new species endemic to the Etowah River system in Georgia, specifically in Long Swamp Creek, Amicalola Creek, and the upper portion of the Etowah River. The earliest collection records for Percina freemanorum date to 1948 and in 2007 the species was delimited as populations of Percina kusha. Our investigation into the systematics of Percina kusha is motivated by the uncertain status of populations in the Coosawattee River system and observed morphological disparity in several meristic traits between populations in the Conasauga and Etowah River systems. Our analyses of morphological divergence, nuclear genotypes, and mtDNA haplotype networks confirm the distinctiveness of Percina freemanorum. Morphologically, Percina freemanorum is distinguished from Percina kusha through lower average numbers of lateral line scales (65.4 vs. 72.3); rows of transverse scales (18.0 vs. 21.4); scales around the caudal peduncle (22.1 vs. 24.9); and modally more pectoral fin rays (14 vs. 13). The two species are not reciprocally monophyletic in phylogenetic analysis of mtDNA sequences, but the two species do not share mtDNA haplotypes. Analysis of up to 158,000 RADseq loci resolve each of the two species as reciprocally monophyletic and genomic clustering analysis of single nucleotide polymorphisms identifies two genetic clusters that correspond to the morphologically delimited Percina freemanorum and Percina kusha.