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Branchinecta lindahli is a generalist fairy shrimp that has a widespread distribution in North America. We initiated a study to better understand the geographic structure of genetic variation within this species and to test if cryptic species are present in B. lindahli. Additionally, we examined four other species of Branchinecta to test if there were any generalities in the levels of genetic divergence within and among species. Genetic data from the mitochondrial cytochrome c oxidase I gene revealed two distinct clades within B. lindahli: one found in the Central Valley and Mojave Desert of California, USA and one found in Baja California, Mexico. The remaining haplotypes were widespread throughout the remainder of North America. Further examination of the distribution within clades revealed no additional phylogeographic structure. The amount of intraspecific divergence observed for B. lindahli and B. hiberna was high compared to B. mackini and B. sandiegonensis. However, maximal intraspecific divergences were less than what was observed among Branchinecta species. We argue that the amount of intraspecific divergence observed in B. lindahli is not consistent with the presence of cryptic species and that caution should be taken when attempting to delimit cryptic species within this group.