The yellowcheek darter, Etheostoma moorei (Raney and Suttkus), is an endemic species of the upper Little Red River, Arkansas. Population estimates over the past two decades have identified an 80% reduction in numbers. Seventeen presumptive loci and six meristic characters were analyzed for 85 individuals to determine the relatedness of populations from three headwater streams. Genetic distances, based on allozyme analysis ranged from 0.000 to 0.213, with each stream population partitioning into distinct subpopulations. Turkey Fork individuals had high genetic distance values from Middle and South Fork individuals. None of the six meristic features studied demonstrated significant differences between stream sites. These findings and previous ecological and life history studies all suggest that the Turkey Fork and Middle/South Fork populations be treated as unique management units.