Gene products of 17 putative loci were analyzed to determine the genetic diversity for 85 individuals of Etheostoma moorei Raney & Suttkus, a darter species endemic to Arkansas, that has been subjected to severe habitat and numerical decline. Number of alleles per locus (1.3), heterozygosity (0.048) and polymorphism (25.9%) values were high relative to those of other darter species. Geographic samples did not exhibit isolation-by-distance, which may be associated with repeated extirpation and recolonization events. Of concern is the high number of polyallelic loci in Hardy-Weinberg disequilibrium (26%), indicative of populations undergoing genetic change. Several causative explanations were investigated with founder effect and inbreeding being the most plausible hypotheses. As these populations continue to decline in numbers, loss of genetic diversity appears imminent.