We have linked phylogenetics with population genetics in order to investigate the effects of development mode on the genetic diversity and population structure of two southern South American marine gastropod species, Crepipatella dilatata and C. fecunda. DNA sequences were obtained for the mitochondrial gene cytochrome oxidase (COI). We have found that the mean level of genetic diversity was significantly greater in C. dilatata than in C. fecunda, the latter having the highest number of shared haplotypes. The AMOVA analysis shows that C. dilatata has a marked population genetic structure, with 56.86% of the observed genetic variation explained by the variation between populations, in contrast to the genetic homogeneity exhibited by C. fecunda in which most of the variance (97.33%) is explained by the intrapopulational variation. For C. dilatata the multimodal curve obtained is consistent with a long-term stationary population model, whereas in the case of C. fecunda, the mismatch distribution shows a significant fit to a population growth model. Both, the level of genetic differentiation among populations as well as the patterns of genetic structure, correlate well with the larval developmental mode. The role of the environment, selection and historical events on the level of genetic differentiation and the population genetic structure are discussed for both species.