Extreme variation in early life-history strategies is considered a moderately good predictor of genetic subdivision and hence dispersal for a range of marine species. In reality, however, a good deal of population differentiation must reflect historical effects, more subtle variation in life histories, and, particularly, the interaction of larvae with oceanographic processes. Using a combination of allozyme and microsatellite markers, we show that the large-scale genetic structure of populations of three species (direct and planktonically developing cushion stars and a planktonic developing sea anemone that is also asexually viviparous) varies consistently, in line with the predicted capacity for dispersal within three geographic regions. We detected high levels of genetic subdivision for the direct developing cushion star (FST = 0.6), low levels for the planktonically developing cushion star (FST = 0.009), and intermediate levels for the sexual/asexual sea anmone (FST = 0.19). These patterns are exhibited despite the highly variable patterns of current movement and the presence of biogeographic barriers. Our results suggest that, although there is large scale genetic differentiation for two species, patterns of population connectivity are remarkably consistent within major regions and do not reflect variation in major oceanographic processes or genetic discontinuity coincident with biogeographic boundaries.