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Aim The Mohave ground squirrel ( Xerospermophilus mohavensis) is one of a few endemic species of the Mojave Desert of south-western North America. We describe phylogeographic patterns within this species and its sister taxon ( Xerospermophilus tereticaudus) and test hypotheses concerning their biogeographical history using genetic signatures of stable versus expanding populations. We compare these patterns with those of other Mojave species to evaluate the role of vicariance in producing phylogeographic structure during the assembly of the Mojave Desert biota. Location The Mojave Desert and adjacent desert regions of south-western North America. Methods Complete cytochrome b gene sequences of X. mohavensis (46 individuals representing 11 localities) and X. tereticaudus (38 individuals representing 14 localities) were analysed using Bayesian methods to infer phylogenetic relationships. Genetic signals of stable or expanding populations were examined based on the distribution of recent mutations and pairwise differences, as well as with a coalescent-based approach. Results The two species are reciprocally monophyletic and may have diverged in response to the late Pliocene–early Pleistocene uplift of the Transverse Ranges and Mojave block. Little phylogeographic structure is evident within X. mohavensis, but there is a signature of northern expansion from a presumably full-pluvial refugium in the Mojave River basin. Four geographic subgroups are evident within X. tereticaudus, and there is a signature of northern expansion from a presumably full-pluvial refugium in the Sonoran coastal plains. Roughly congruent phylogeographic patterns are found within five arid-adapted taxa, indicating a strong element of vicariance during the assembly of the generally transitional Mojave Desert biota. Main conclusions We present a preliminary model for the historical assembly of the Mojave Desert biota that indicates a strong vicariant element producing autochthonous lineages (including X. mohavensis) that diverged during the major geological and climatic events of the last 5 Myr. Phylogeographic partitioning within the Mojave Desert underscores the necessity of immediate conservation measures for this unique and fragile arid ecosystem that is locked between two large metropolitan population centres and is the target of continued adverse environmental impact. [ABSTRACT FROM AUTHOR]