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Genetic structure in the marine environment can show patterns consistent with expectations of life history, geography, and ocean circulation. Organisms with direct development often have low dispersal rates and high potential for local adaptation. Leptasterias is a genus of six-rayed sea stars with direct development and multiple clades forming cryptic species complexes on the eastern Pacific coast. The L. aequalis complex is comprised of several clades found on the central California coast in intertidal and subtidal habitats. Using DNA sequence data from portions of the mitochondrial putative control region and 16S, we show here that a previously undescribed and genetically distinct lineage of Leptasterias inhabits intertidal sites in close proximity to the San Francisco Bay estuary, while geographically separated yet genetically similar clades are located to the north and south. The San Francisco Bay estuary might act as a phylogeographic barrier to dispersal and localized environmental features of San Francisco Bay outflow might shape opportunities for differentiation by further partitioning Leptasterias populations. [ABSTRACT FROM AUTHOR]