Here we predict oceanographic connectivity among four geographical locations in the south west of Western Australia using hydrodynamic modelling of larval dispersal and test these predictions against genetic descriptions of population structure, population boundaries and estimates of larval migration in two co-distributed sea urchin species. Sea urchins are excellent models for characterising marine population connectivity because of their commonness, diversity of larval life histories, ease of sampling, and ecological importance as grazers in coastal benthic habitats. Our study sampled two species, Heliocidaris erythrogramma and Phylocanthius irregularis. H. erythrogramma spawns predominantly in summer and its lecithrotrophic larvae are free swimming for 3-4 days in laboratory observations. In contrast, little is known about spawning time and larval duration in P. irregularis. The south-west corner of Australia is dominated by the Leeuwin current system, the worlds only poleward-flowing western continental boundary current. The Leeuwin current (LC) is particularly strong in the late autumn and winter months and is weaker in the summer. Strong seasonal contrasts in the LC flow pattern make it possible to generate testable predictions about the predominant direction of larvae-mediated gene flow in H. erythrogramma. Comparison of genetic structure with oceanographic model predictions allowed us to make predictions about the possible larval biology of the less well characterised urchin P. irregularis.