The Tallapoosa darter (Etheostoma tallapoosae) is only found in the Piedmont portion of the Tallapoosa River system which spans Georgia and Alabama. Particularly in western Georgia headwaters, the habitat of this darter is potentially threatened by human population growth. The purpose of this study was to assess the extent of genetic variation and genetic structuring of this species to determine if those populations at greatest risk are genetically unique and would thus raise conservation concerns. Mitochondrial control region and cytochrome b sequences were determined for thirteen populations spanning the length of this species' range. Phylogenetic analysis and analysis of molecular variance shows that while the populations in western Georgia headwaters are not genetically unique, the Tallapoosa darter population is subdivided into genetically divergent populations that can be designated as management units for future monitoring of the species.