Temporal changes at 16 allozyme loci in the Diplodus sargus population of Banyuls-sur-Mer (Mediterranean Sea, France) were monitored. Temporal genetic variation within a single population was examined over two temporal scales: (i) among three year-classes sampled at the same age, and (ii) within a single year-class sampled three times over a two-year period. We observed a significant change in the genotypic structure within the same cohort during the first two years following settlement and before recruitment into the adult population. In addition, comparison of year-classes showed that cohorts differed significantly one year after settlement, whereas they became similar later on before recruitment into the adult population. The observed changes in the genetic structure within and between year-classes may be the result of complex selective processes or genetic drift. Linkage disequilibrium and genetic relatedness data suggest that these changes are due to large variation in reproductive success, followed by homogenization through adult movement. Overall, these results demonstrated a rapid genetic change within a population.