The distribution of the Dark Kangaroo Mouse, Microdipodops megacephalus (Rodentia: Heteromyidae), is limited exclusively to sandy habitats within the hydrographic Great Basin region of western North America. The phylogeography of populations of M. megacephalus were examined throughout its distribution using mitochondrial DNA (mtDNA) sequence data. The 16S rRNA gene (550 bp) was analyzed for 101 individuals from 35 separate localities, and phylogenetic trees (neighbor-joining distance, parsimony, and maximum likelihood) were constructed using these data. The results of these trees, while preliminary, depict patterns of relationship suggesting a strong northwest-southeast division within the distribution of M. megacephalus . A 3.38% sequence divergence (uncorrected p) supports these northwestern and southeastern evolutionary units. Detailed phylogeographic information about M. megacephalus and other sand-obligate organisms is needed for informed habitat management. These phylogenetic patterns are evaluated in the context of the historical biogeography of the species.