The geomorphological formation of the Baja California peninsula and the Gulf of California, along with its associated islands, has created a dynamic stage for the evolution of squamate reptiles since the Late Miocene. Most published phylogeographic studies of Baja California snakes and lizards have relied on mitochondrial DNA sequence data only, but as nuclear DNA sequence data has become common, the shortcomings of mtDNA-only studies have become evident. Introgression, the movement of genetic markers across lineage boundaries, has been documented with particularly high frequency for the mitochondrial genome. Nuclear loci can experience introgression as well. Studies of lineage boundaries can be misled and multilocus phylogenies distorted when failing to account for both nuclear and mitochondrial introgression. In Chapter One of this dissertation, I investigated whether mitochondrial introgression has led to an incorrect understanding of phylogenetic relationships among alligator lizards in the genus Elgaria, with a particular focus on the placement of the taxon E. panamintina. Using DNA sequence data from three mitochondrial fragments and seven nuclear loci, coalescent-based phylogenetic tools were used to infer a species tree. By modifying previously developed methods, I applied two novel tests of introgression. While I did find that introgression has misled previous phylogenies, the recovered introgressive events were not those hypothesized at the onset of this study. In Chapter Two, I performed a multilocus phylogeographic study of the Western Banded Gecko, Coleonyx variegatus, using two mtDNA fragments and four nuclear exonic regions. Specifically, I evaluated the role of the geological formation of the northern Gulf of California as it relates to the divergence of peninsular and continental populations. While the mtDNA gene tree failed to recover clades corresponding to either group, both clustering and coalescent-based analyses of the combined nuclear data did recover the two groups. Discordance between the mtDNA gene tree and nuclear-based species tree was found to be the result of repeated mitochondrial introgression. In Chapter Three, I investigated secondary contact between peninsular and continental lineages of banded geckos in northeastern Baja California. There the Desert Banded Gecko (C. v. variegatus) and the San Diego Banded Gecko (C. v. abbotti) have been hypothesized to genetically interact in a neutral hybrid zone. Analyzing secondary contact with one mtDNA fragment and five nuclear loci using gene tree reconstruction and clinal analyses, I located an abrupt, narrow hybrid zone. Gene flow was bidirectional but limited, and wakes in the clines of the nuclear loci demonstrate patterns consistent with hybrid zone movement as C. v. variegatus expanded its range southward. Mitochondrial introgression in the opposite direction may be the result of selection, however.