The vernal pool fairy shrimp Eubranchipus vernalis (Eastern Fairy Shrimp) is an obligate freshwater invertebrate that is an important member of northeastern United States vernal pool ecosystems. The extent of gene flow among populations of vernal pool fairy shrimp in the Northeast is currently unknown, yet this information is important for understanding the ecology and evolution of this species. In order to infer the level of gene flow among E. vernalis populations, we used mtDNA sequence data to estimate the level of genetic divergence and the pattern of geographic variation among 22 vernal pool populations sampled across Massachusetts during spring 2003. We found significant differences among vernal pool populations in the frequency of unique mtDNA sequences, but no coherent geographic pattern in the distribution of these sequences, and there was no significant correlation between levels of genetic divergence and geographic distance. We argue that these results reflect priority effects rather than limited dispersal among these populations.