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Aim Recently discovered deep phylogenetic gaps in coastal California marine taxa are geographically discordant with the provincial biogeographic boundary at Point Conception. This discordance runs contrary to the phylogeographic hypotheses that were derived from studies of coastal marine taxa in south-eastern North America. Here, I investigate the nature of the discrepant phylogeographic and biogeographic patterns in coastal California.Location Coastal south-western North America.Methods The scientific literature describing the phylogeography and biogeography of coastal California taxa was reviewed. Data describing life-history characteristics, habitat, and degree of phylogeographic structure were extracted and compared. The geographical distribution of phylogenetic breaks was compared with regional biogeographic data.Results All taxa were genetically variable. Those with greater dispersal ability generally had less phylogeographic structure. Although few taxa had very limited dispersal ability, many exhibited phylogeographic breaks within the California Transition Zone, a region of gradual species replacement between Oregonian and Californian biogeographic provinces. The most precisely resolved phylogeographic breaks were geographically concordant with peaks in the distribution of edge-effect species, which are strong indicators of environmental discontinuities, or ecotones. Moreover, these phylogeographic gaps, edge-effect species, and ecotones coincide geographically with Late Pleistocene faunal discontinuities and probable long-term physical barriers to gene flow.Main conclusions Contrary to prior inference, phylogeographic patterns in coastal California marine taxa are consistent with the phylogeographic hypotheses. The concordance of phylogeographic and biogeographic patterns in the coastal marine faunas of south-eastern and south-western North America, and also the Indo-Pacific, suggests that the phylogeographic hypotheses are generally applicable to many coastal marine settings. As such, they provide a framework for investigating and comparing patterns of evolution in disparate coastal marine faunas.