The salamander Ensatina eschscholtzii is a classic example of a ring species, and has an intricate biogeographic history. Within a part of the ring distribution, earlier work using allozymes disclosed high levels of genetic structure in central coastal California, where the subspecies oregonensis, xanthoptica, and eschscholtzii meet. We used mitochondrial cytochrome b sequences to further examine patterns of divergence in this area, including data from 155 localities (309 individuals). Our focus is on the documentation of population-level haplotype lineages. We show that oregonensis is represented by two unrelated, phenotypically similar clades, both of which possess substantial substructure of their own. The subspecies xanthoptica includes two lineages that differ in phenotype, one of which has colonized the foothills of the Sierra Nevada. The subspecies eschscholtzii occurs mainly to the south, but some populations from a northern lineage extend into the Monterey Bay region, where they approach xanthoptica geographically. In sum, populations in the central coastal California region form a distributional patchwork, including three subspecies, three clades (which differ from the three subspecies), and ten haplotype lineages. We conclude that such striking levels of phylogeographic structure reflect interspersed episodes of spatial fragmentation, in part driven by the complex geomorphological evolution of the California Coast Range system.