Crepidula dilatata (Lamark, 1822) and Crepidula fecunda (Gallardo, 1979) are sympatric species in southern Chile. Separating them by species is difficult because they are morphologically similar; an important character, which separates them is their comparative larval development. C. dilatata includes nutritive eggs within its egg capsules that are consumed by larvae in the capsule during their intracapsular development. Metamorphosis occurs in the capsule, followed by the hatching of crawling juveniles. The C. fecunda intracapsular development leads to the release of planktotrophic veliger larvae that persist in the water column for about 15 days prior to settlement and metamorphosis. These two contrasting reproductive strategies (direct and indirect development) may influence the capabilities of these species for dispersal, which could influence their comparative gene flow and population genetics. Newly developing molecular genetic techniques, such as RAPD used in the present study, were useful in identification of the two species studied and provided some initial data on their comparative population genetics. Greater gene flow and interpopulational gene diversity were found in C. fecunda (pelagic larva) compared with C. dilatata (direct development), with the latter showing populations to be the more genetically heterogeneous within the geographic range studied. It was thus evident that the pattern of larval development (direct or planktonic) influenced the comparative population genetic structure between these two species.