To estimate levels of gene flow over short distances (less than a few kilometers) in the fairy shrimp, Streptocephalus texanus, mitochondrial DNA sequences (part of the cytochrome oxidase locus) were examined in 98 individuals from 13 populations near Moab, Utah. Populations were arranged linearly along two transects on slickrock ridges, and one isolated population about 2–3 km from the others. We found six haplotypes, differing from one another by 1 to 23 nucleotides. Nucleotide diversity among the nine populations from the MiVida ridge was 0.0019 with no isolation by distance. The three populations from the Sand Flat ridge were fixed for the same haplotype, not found in other populations. The isolated population (loop B pool) contained two haplotypes, one of which was very different from others in the study. The general pattern was little differentiation among populations separated by less than about 1 km, with more differentiation at greater distances. This is consistent with passive dispersal of cysts by wind over short distances, and rare long-distance dispersal.