In cyclical parthenogens, clonal diversity is expected to decrease due to selection and drift during the asexual phase per number of asexual generations. The decrease in diversity may be counteracted by immigration of new genotypes. We analysed temporal variation in clonal diversity in colonies of the monophagous tansy aphid, Macrosiphoniella tanacetaria (Kaltenbach), sampled four times over the course of a growing season. In a related field study, we recorded aphid colony sizes and the occurrence of winged dispersers throughout the season. The number of colonies increased from April, when asexual stem mothers hatched from the sexually produced eggs, to the end of June. The proportion of colonies with winged individuals also increased over this period. After a severe reduction in colony sizes in late summer, a second expansion phase occurred in October when sexuals were produced. At the season's end, the only winged forms were males. A linked genetic study showed that the number of microsatellite multilocus genotypes and genetic variability assessed at three polymorphic loci per colony decreased from June to October. Overall, the relatedness of wingless to winged individuals within colonies was lower than average relatedness among wingless individuals, suggesting that winged forms mainly originated in different colonies. The results demonstrate that patterns of genetic diversity within colonies can be explained by the antagonistic forces of clonal selection, migration and genetic drift (largely due to midsummer population bottlenecks). We further suggest that the males emigrate over comparatively longer distances than winged asexual females.