Recent studies of intraspecific phylogeography have suggested that the geographic location of genetic discontinuities, or phylogeographic breaks, may frequently coincide with biogeographic boundaries. The concordance is hypothesized to reflect similarity in the processes governing species boundaries and intraspecific lineage boundaries. This concordance has not, however, been widely tested. In the case of the Point Conception biogeographic boundary between the Oregonian and Californian marine biotas, only the supralittoral copepod Tigriopus californicus has been found to have a coincident phylogeographic break. Here I show that the apparent relationship between this break and Point Conception was, in fact, an artifact of insufficient geographic sampling. Mitochondrial DNA analyses of T. californicus populations between Morro Bay and San Diego reveal at least five equally deep phylogeographic breaks in the region (where only one biogeographic boundary is recognized). Limited nuclear DNA sequence data and allozyme data also support the occurrence of multiple genetic discontinuities along this geographic range. Lack of one-to-one correspondence between intraspecific phylogeography and biogeographic boundaries indicates that the processes affecting the genetic differentiation of populations of T. californicus differ from those responsible for determining species distributional limits at the Point Conception biogeographic boundary. A review of genetic data from other species also fails to provide evidence for concordance of biogeography and intraspecific phylogeography across Point Conception. I suggest that the concordance of phylogeography with biogeography will only be pronounced where the biogeographic boundary separates biotas that are phylogenetically related. The numerous cases of interspecific hybrid zones in the region of Cape Canaveral, for example, indicate that many sister-species pairs occur across this biogeographic boundary. Such hybrid zones are not common at Point Conception, and there appears to be no cases of intraspecific phylogeographic breaks associated with this well-recognized biogeographic boundary.