Understanding positive interactions among species is integral to predicting the outcomes of community-level dynamics. Few studies have explored intraspecific variation in positive associations. We investigated facilitation between two coastal dune shrubs in California, Baccharis pilularis and the nitrogen-fixing species, Lupinus arboreus. L. arboreus seedlings and adults were non-randomly distributed, occurring most frequently in association with B. pilularis. The relationship depended on the genotype of B. pilularis; only the prostrate architectural form of this species was positively associated with L. arboreus. To evaluate the nature of this association, we assessed the influence of three microhabitat types (prostrate B. pilularis, Ammophila arenaria (an introduced dune grass), and exposed sand) on four life history stages of L. arboreus. Prostrate B. pilularis benefited L. arboreus seedling emergence, survival, and growth but had no effect on post-dispersal seed predation or adult establishment. Enhanced resistances to granivory by rodents or to seedling predation by voles were not important mechanisms underlying facilitation. In addition, an experiment manipulating herbivory by cutworms found no effects of microhabitat on susceptibility to damage. Evidence supports the hypothesis that the prostrate form of B. pilularis facilitates L. arboreus germination, seedling growth, and establishment as compared to exposed sand and dune grass. Furthermore, in combination with prior research, the results suggest that by facilitating an important nitrogen-fixer, B. pilularis may have effects that cascade to other members of the coastal plant community.