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The family Heteromyidae includes 6 genera of rodents traditionally placed in 3 subfamilies endemic to the Nearctic and northern Neotropical biogeographic regions. Although several of these taxa represent intensively studied members of North and Central American ecosystems (e.g., kangaroo rats and pocket mice), phylogenetic relationships within and among subfamilies, genera, and species-groups are not well understood. Here, we used maximum-likelihood, Bayesian, and maximum parsimony analyses of sequence data from 2 mitochondrial DNA genes, the cytochrome oxidase subunit 3 gene (699 base pairs [bp]) and the cytochrome-b gene (1,140 bp), to investigate phylogenetic relationships among 55 species-level taxa. We found robust support for monophyly of genera Dipodomys, Microdipodops, Chaetodipus, and Perognathus; sampling of Liomys and Heteromys was inadequate to evaluate their …