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Restriction‐endonuclease‐site variation of mitochondrial DNA (mtDNA) was used to investigate patterns of geographic and phylogenetic divergence within the rodent genus Onychomys. Onychomys has occupied arid habitats in the western North American deserts, shrub‐steppes, and grasslands since the late Tertiary. A phylogenetic analysis of the total mtDNA restriction‐site variation throughout the range of Onychomys suggests that the distribution of this genus has been affected by the same Quaternary pluvial‐interpluvial climatic fluctuations that have resulted in the periodic fragmentation of arid habitats in western North America. Onychomys mtDNA haplotypes define at least five discrete geographical subsets, suggesting that there are five areas of endemism for biota restricted to arid and semiarid habitats in North America. The mtDNA‐haplotype phylogeny can be used to infer an hypothesis of historical …