In marine organisms, a pelagic larval stage increases the opportunities for long–distance dispersal and is often associated with little genetic differentiation over large geographical distances. Here we test the hypothesis that early life–history characteristics, including larval spatial distributions, affect the rates of dispersal and, therefore, the levels of genetic partitioning among three Gulf of California reef fishes: Axoclinus nigricaudus, Malacoctenus hubbsi; and Ophioblennius steindachneri;. These three blennioid fishes have markedly different early life histories: A. nigricaudus has a short larval duration (18 days) and develops inshore, M. hubbsi has an intermediate larval duration (24 days) and most individuals develop inshore and O. steindachneri has a long larval life (50 days) and disperses offshore. Estimates of genetic partitioning from mtDNA control region sequences differed greatly between these species and were in the same rank order as predicted by their early life-history characteristics (A. nigricaudus N_ST=0.536, M. hubbsi N_ST=0.261 and O. steindachneri N=0.000). These results indicate that larval strategies may be good predictors of population genetic structure in some marine fishes.