This study used fine-scale phylogeography of populations of side-blotched lizard, Uta stansburiana to determine concordance with previously identified phylogeographic patterns in the Transverse Mountain Range of Southern California. Mitochondrial DNA analysis revealed clade distributions that both agreed and conflicted with previously identified clade breaks. This study revealed two new distinct clade breaks that transect the San Gabriel Mountains and detected haplotype mixtures in populations sampled between the San Gabriel and San Bernardino Mountains. Genetic landscape GIS analyses identified areas of genetic divergence and diversity for this species. This combined analysis enabled the discovery of a suture zone between the San Gabriel and San Bernardino Mountains that represents a phylogenetic crossroads with high levels of diversity and divergence and complex phylogeographic structure. My results suggest the importance of the use of fine-scale phylogeographic analysis in the discovery of new clade boundaries within a geologically complex and hyper-diverse region.