The Rosy boa (Lichanura trivirgata) is found throughout the semi-arid and arid regions of southwestern North America. Threats from various factors have raised concern regarding the long-term survival of many populations, particularly within southern California (a region where populations are highly fragmented). This study examines the phylogeography, population structure, and taxonomy of the Rosy boa across its geographic range through phylogenetic analysis of ~ 1100 bp of mitochondrial DNA sequence data. An intraspecific phylogeny was reconstructed from 102 snakes using a combined procedures approach (i.e. statistical parsimony and maximum likelihood), and nested clade analysis was used to help discriminate between evolutionary patterns operating at the population level. The phylogeny reveals significant geographical structuring of haplotypes and three distinct regional lineages (Baja California, Arizona, and California) across the range of Lichanura. Diversification between these lineages appears to have developed over differing time frames: (1) a basal divergence indicating long temporal discontinuity between the Baja California and Arizona + California lineages, and (2) a more recent divergence event between Arizona and California lineages. Nested clade analysis of California populations shows a strong recurrent pattern for restricted gene flow with isolation by distance across the entire regional lineage. The geographically subdivided and divergent nature of the Lichanura populations is suggestive of a general phylogeographic model of regional divergence, with the potential for gene flow between populations within a region but isolation between regions.