Cyclically parthenogenetic rotifers are a valuable model for investigating the relationship between reproductive mode and population structure, although advances in this field have been hindered by low allozyme variability in these organisms. A high genotypic diversity is predicted after population establishment, which would be eroded by clonal selection during the parthenogenetic phase. The resting egg bank, produced sexually, is presumed to store high levels of genetic diversity, with subsequent effects on planktonic population structure. Here, we provide the first application of microsatellite markers to a rotifer planktonic population and its associated resting egg bank. Seven polymorphic microsatellite loci were screened in populations of the rotifer Brachionus plicatilis in a temporary pond to analyse: (i) the genetic structure of the resting egg bank; (ii) the changes in the genetic structure of rotifer populations during the parthenogenetic phase; and (iii) the population structure after its initiation from resting eggs. Microsatellites proved to be a useful tool for clone identification, revealing a surprisingly high clonal diversity in rotifer populations. The last sample in the parthenogenetic phase showed evidence of clonal selection, as indicated by a low observed clonal diversity and the appearance of linkage disequilibria. The resting egg bank, analysed comprehensively for the first time in any zooplankter, is in Hardy–Weinberg and linkage equilibrium, and contains a high genotypic diversity. Unexpectedly, the resting egg bank differed from the planktonic population in its allelic composition, suggesting that resting egg hatching is biased.