Population genetic data are becoming an increasingly important tool in the conservation and management of endangered species. Statistical analysis of genetic data can inform agencies on population boundaries within a species, and help to infer processes that lead to genetic patterns, thereby influencing conservation decisions. This thesis examines population genetics in the endangered San Diego fairy shrimp, Branchinecta sandiegonensis, using multiple molecular markers. In order to quantify diversity and population structure, genetic data were collected from 50 pools from 23 pool complexes scattered throughout San Diego County at seven novel microsatellite loci. We tested the hypothesis that pool complex boundaries and geographic distance are important components of genetic structure. Microsatellite and mtDNA genetic patterns were compared to test for concordance between marker types. We also conducted preliminary tests for the effect of pool disturbance and hybridization on genetic diversity. Overall, results show that there is considerable microsatellite diversity within pools. In the preliminary tests, no significant change in genetic diversity in response to hybridization was detected. Disturbance may affect genetic diversity within pools, but it is unclear which component of disturbance is correlated with diversity. Overall, genetic differentiation among pool complexes is relatively strong. The hierarchical spatial arrangement of pools plays a significant role in genetic divergence among populations. Increasing geographic distances between sites is a significant gene flow barrier for this species, as has been found for other fairy shrimp species. Evidence of historical isolation between two divergent groups was also found. There is concordance among marker types, with some discrepancies. Population genetic structure in B. sandiegonensis across the study range is governed by gene flow restricted primarily to pool complexes. We recommend that pool complexes be treated as management units provided that pools are ecologically similar within them. Historical divergence among groups of pools should be taken into account as well, in order to maintain genetic variation and dispersal mechanisms across the species' range.