The peach-potato aphid, Myzus persicae (Sulzer), has a complex reproductive mode in which some lineages reproduce by continuous parthenogenesis, whereas others reproduce sexually once a year. The climate is thought to act directly on the reproductive mode, because sexual eggs are the only form that can resist frost in cold regions. Sexual reproduction necessitates an obligatory host alternation that may result in long-distance dispersal. Here, we examined the genetic variability at seven microsatellite loci of populations of M. persicae in France, where both reproductive modes occur. We provide clear genetic evidence that the breeding system affects genotypic variability, as cyclically parthenogenetic aphids are far more variable than their obligately parthenogenetic counterparts. A temporal decrease in genetic variability and a temporal genetic differentiation effect suggest the existence of selective factors that play an important role in shaping the genetic structure of M. persicae populations. Lastly, differences in the population structure between reproductive modes suggest that the migration associated with the change of host during sexual reproduction lowers the level of population differentiation.