Clonal reproduction is commonly incorporated into the life cycles of many metazoans. However, whether and how such highly clonal animals persist in the face of natural enemies remains poorly understood. Here we report the first temporal genetic study of a clonal population, the freshwater bryozoan Cristatella mucedo, and the associated prevalence of a myxozoan parasite. High levels of both clonality and parasitism persisted over a 3 year period. Random amplified polymorphic DNA markers revealed four distinct clones of C. mucedo. The two most common clones varied in abundance with the significantly more common clone in the first year becoming the significantly less common by the third year. There was no evidence that the most common clone was disproportionately infected. These results are discussed in relation to predictions of the Red Queen and the metapopulation dynamics of clonal organisms.