Cyprinella gibbsi (Tallapoosa shiner) is sympatric with Etheostoma tallapoosae (Tallapoosa darter) and both species are endemic to the Tallapoosa River system of Georgia and Alabama. The darter population has been shown to be divided into genetically divergent populations. In this study, mitochondrial ND4L sequences were analyzed for 10 populations of the Tallapoosa shiner from throughout its distribution. Phylogenetic analysis and analysis of molecular variance show that the shiner population is also divided into genetically divergent populations. These can be designated as management units for future monitoring of the species. The distributions of the genetically divergent populations of the shiner and the darter are similar, and indicate that the two species share a common biogeographic history.