The San Diego fairy shrimp (Branchinecta sandiegonensis ) is listed as federally endangered as a result of large-scale urbanization and subsequent vernal pool habitat loss. When new pools are created for mitigation or disturbed pools are restored, sediment from existing pools may be used for inoculation. The success of these projects can depend on whether source material is taken from a gene pool that is differentially adapted from the destination. Previous studies have suggested that there are at least two regional gene pools of San Diego fairy shrimp within San Diego County. A putative contact zone between these gene pools occurs primarily on land owned by the Marine Corps Air Station at Miramar (MCAS Miramar). We collected adult fairy shrimp from 51 pools across MCAS Miramar and extracted DNA from 1752 individuals. Using the mitochondrial gene cytochrome oxidase I (COI) in conjunction with seven microsatellite loci, we delineated the gene pool boundary with greater precision than was previously known. We also tested for additional population structure within each of these regional gene pools, based on a variety of poolspecific and landscape features. Both COI and microsatellite results were largely concordant at our study site and showed two gene pools with a distinct geographic break. Undisturbed pools were fixed for one gene pool, but disturbed pools showed greater admixture between the two genetic groups. The distinct geographic break between the two gene pools coincided with a large canyon on our study site. Isolation by distance analyses supported the canyon as a barrier to gene flow after we controlled for geographic distance. In addition, landscape genetic analyses showed presence of roads as a barrier to gene flow between pools. We designated six management units on MCAS Miramar, which will allow us to maintain species integrity, maintain the two regional gene pools, and maintain the integrity of complexes that show unusually high divergence. To best ensure the continued success of this endangered species, we recommend that inoculation of new pools use soil from within the same management group.