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The phylogeographic structure of some species distributed across the Baja California Peninsula has been traditionally hypothesized as resulting from vicariant events thought to have occurred between 1-3 Mya. Climatic fluctuations during the Pleistocene have also been shown to influence the distribution patterns of species, and vicariant patterns may have been erased as a consequence of population contractions or expansions into or out of refugia generated during the last glacial maximum ca. 21,000 years ago. Thus, there is still some uncertainty regarding the relative role of vicariance in shaping the modern biota of Baja California. To understand the evolutionary history of the wolf spider Pardosa sierra Banks, 1898 on the peninsula, a phylogeny of this species and closely related taxa was generated using a fragment of the mitochondrial gene cytochrome c oxidase subunit I (CO1). Sequences of a fragment of the CO1 gene for 38 individuals from 14 sampling sites along the entire distribution range of P. sierra were used to infer phylogeographic patterns, and five nuclear microsatellite loci were also used to genotype 296 individuals from seven of these 14 locations. The current and past potential distributions from two Pleistocene periods were estimated using niche-based distribution modeling, and scenarios of colonization from detected refugia were simulated. We found that Californian populations of P. sierra diverged from peninsular populations 4 Mya, this divergence coinciding with the northern-gulf split. However, we did not detect genetic breaks in regions where the mid-peninsular and Isthmus of La Paz canals were presumably formed, either with mitochondrial DNA sequences or microsatellite loci. Two refugia were further detected at the geographic ends of the peninsula, these likely preceding subsequent habitat expansion.