The California killifish, Fundulus parvipinnis, is a marine species that lives in salt marshes, estuaries and wetlands along the California and Baja California coasts. In order to estimate levels of dispersal between different coastal habitats over its range, we have studied six populations using morphological and genetic markers. Lateral line scale and vertebrae counts showed significant differences between individuals collected north of Punta Eugenia and south of Punta Eugenia. Morphological differences across Punta Eugenia were accompanied by large genetic differences at the mitochondrial control region (5.8%). Gene flow was in general very reduced over the range of the species (pairwise average F(st)=0.70, Nm=0.30), with a strong break at Punta Eugenia (F(st)=0.95, Nm=0.03). Such limited interchanges between coastal habitats have important theoretical and conservation implications.