The complex geology of southern California is an important mechanism that drives lineage isolation and promotes high levels of inter- and intraspecific variation. This, in combination with anthropogenic habitat fragmentation, potentially threatens a host of endemic animals and plants in this biodiversity hotspot region. The endemic California “bear scarabs” offer a model for examining highly variable lineages, allowing us to elucidate evolutionary mechanisms that generate variation and understand threats to biodiversity. The phenotypically variable Paracotalpa ursina species complex is assessed using a combination of DNA data (nuclear AFLP and mitochondrial sequences), morphology, and distribution modeling. I use molecular data to examine discontinuities between populations and investigate the role of geography and urban centers in genetic isolation among P. ursina morphotypes. All data sets suggest that the Transverse Mountain Ranges in California form a biogeographic barrier isolating populations and acting, in part, as a mechanism that promotes variation. Based on these results, two groups in the P. ursina species complex are identified: Paracotalpa ursina (Horn, 1867) (northern group) and Paracotalpa rotunda (Casey, 1915) (southern group). As a result, the following are considered synonyms of P. ursina (Horn): Paracotalpa seriata (Casey, 1915) and P. ursina piceola Saylor, 1940. The following names are considered synonyms of P. rotunda (Casey): Paracotalpa brevis (Casey, 1915), P. laevicauda (Casey, 1915), P. rubripennis (Casey, 1915), P. nigripennis (Casey, 1915), and P. leonina (Fall, 1932). A key to the five species of Paracotalpa is presented and based on non-variable species characteristics. Results demonstrate that AFLP genotyping assists in revealing cryptic species in beetles.