It has been suggested that parasites are a strong selecting force for their hosts and therefore may alter the outcome of competition among host genotypes. We tested the extent to which parasite-mediated selection by different parasite species influenced competition among clones of the cyclic parthenogen Daphnia magna. We monitored clone frequency changes in laboratory microcosm populations consisting of 21 D. magna clones. Parasite treatments (two microsporidians, Glugoides intestinalis and Ordospora colligata) and a parasite-free control treatment were followed over a nine-month period. A further treatment with the bacterium Pasteuria ramosa failed. We found significant differences in clonal success among the treatments: the two parasite treatments differed from the control treatment and from each other. Additionally, we measured the clone-specific population carrying capacity, competitive ability against tester clones, and reproductive success of infected and uninfected females to test whether they correlate with clonal success in the microcosms. The clone-specific competitive ability was a good predictor of clonal success in the microcosms, but clonal carrying capacity and host reproductive success were not. Our study shows that parasite-mediated selection can strongly alter the outcome of clonal competition. The results suggest that parasites may influence microevolution in Daphnia populations during periods of asexual reproduction.