Biogeographic patterns have long been studied with the use of mtDNA. Advancements in laboratory techniques have allowed for the accumulation of sequence data from multiple independent nuclear loci to further understanding of biogeographic processes on the genome. This study incorporates five independent loci and integrative approaches to investigate phylogeographic patterns and speciation in the Aspidoscelis hyperythra complex across the Baja California Peninsula. Coalescent-based species tree analyses were used to determined optimal species delimitation. Five of the six insular species in the A. hyperythra group are shown to be valid and A. espiritensis is synonymized with A. hyperythra. This result is corroborated through the genetic cohesion of A. hyperythra by high levels of gene flow between major mitochondrial and insular lineages. The mitochondrial genealogy is misleading and renders A. hyperythra polyphyletic with respect to insular species. However, five major mtDNA lineages of peninsular A. hyperythra are found with most lineage boundaries concordant to those found in other studies in the region. These peninsular lineages are not supported in nuclear genealogies but assignment tests and combined distance-based methods support some of these patterns. By combining mitochondrial and nuclear DNA sequence data this study shows mtDNA patterns in the A. hyperythra complex are broadly consistent with others in the Baja California Peninsula, although the order of lineage diversification differs. Additionally, sole reliance of mtDNA would have mislead species delimitation and assignment, but the inclusion of nuclear data and modern coalescent analyses allows for testing of previously hypothesized species limits and resolution of relationships in the A. hyperythra complex.