Due to their properties for resolving patterns of population genetic structure, microsatellites are increasingly used in studies of breeding systems. Here, eight polymorphic microsatellite loci were isolated and characterized in the aphid Rhopalosiphum padi , in which populations show a mixture of cyclically and obligatory parthenogenetic lines. These loci were then applied to distinguish between 55 parthenogenetic lines of R. padi collected across France. Interestingly, they allowed to detect several copies of the same genotypes among the sample, confirming the great sensitivity of microsatellites and their usefulness in population genetic studies of parthenogenetic organisms.