The kangaroo rat Dipodomys merriami occurs widely over the Baja California peninsula, inhabiting all the arid and sandy lowlands. Its range encompasses diverse climatic, edaphic, and vegetation zones, including 2 islands. The 11 taxa recognized in the merriami complex in this region almost 50 years ago remain valid to the present. The 2 island forms originally were described as different species, and have been treated in different ways by subsequent authors. In this investigation we used a genetic analysis of 2 mitochondrial genes, cytochrome b (Cytb) and cytochrome c oxidase subunit III (COIII), to study patterns of genetic structuring in this species throughout the peninsula. We supplemented existing morphometric and pelage color data with new data, and integrated these data sets into a phylogenetic analysis. Finally, we explored how our results compared with the existing taxonomic arrangement of species and subspecies. Our phylogenetic analyses of molecular data used the concatenation of 1,140 base pairs (bp) of the Cytb gene and 690 bp of the COIII gene; cladograms were generated using maximum-parsimony, maximum-likelihood, and Bayesian inference procedures. A hierarchy of nested clades was produced, the highest level of which revealed 2 reciprocally monophyletic clades separated by 20 mutational steps. There is a Southern Clade extending north to the Vizcaíno Desert in the west and San José Island in the east, and a Northern Clade that includes all the populations farther to the north. At a shallower level, the Southern Clade contains 4 subclades, including the populations of San José and Margarita islands, whereas the Northern Clade is composed of 3 subclades. Adding the morphometric and pelage coloration data sets to the analyses resulted in support for the 11 previously recognized taxa arranged in a single species, Dipodomys merriami, but with improved understanding of how the subspecies relate to each other. As is increasingly appreciated, our investigation supports a comprehensive approach involving multiple data sets that are sensitive to a wide temporal range of evolutionary history for phylogenetic reconstruction.