Lepidomeda vittata (the Little Colorado River spinedace) is a cyprinid fish native to the Little Colorado River in Arizona. Mitochondrial DNA and allozymes were used to determine patterns of genetic variation in remaining populations of L. vittata. The pattern of variation observed indicated that genetic diversity was low, but population structure was high because of partitioning of genotypes among samples. Similarity of genotypes suggest current populations are relics from a single, large population that was one continuously distributed throughout the LCR drainage. Patterns of variation were consistent with decreases in population size; however, because of low levels of variation, it was impossible to determine whether the decline occurred during the past century or a larger time scales.