Nowadays, PCR-based DNA markers allow the study of diversity and differentiation of marine organisms at different stages of their life cycle. Our study of European flat oyster (Ostrea edulis) populations has aimed to describe their spatial and temporal dynamics. First, we analyzed adults sampled over the natural range of the species. An Atlantic/Mediterranean differentiation pattern was observed. Results were congruent between allozymes, microsatellites and mitochondrial DNA and support an isolation by distance model. High variability was observed in the breadth of diversity between populations using a mitochondrial marker, this highlights the small effective population sizes in some locations. A 10-fold quantitative difference was observed in Fst between the genomes, which may be due to an unbalanced sex ratio and/or differential reproductive success. Secondly, we investigated the dynamics of reproduction at a finer scale. Several experiments were performed to study (1) the variance of allele frequencies during a natural settlement period, (2) the paternal contribution to fertilization by analyzing larvae sampled at the brooding stage within individual females, (3) the individual reproductive success within an experimental population. The significance of our results will be discussed in terms of management of the genetic diversity and the potential impact of aquaculture and hatchery propagation.