The amount of genetic variation within a host population may affect the ecology and evolution of pathogen populations. Mixtures of hosts are known to control epidemics of pathogens on crop plants and have been studied extensively in agricultural systems. Surprisingly, the effect of host genetic variation on the spread of animal pathogens has been studied relatively infrequently. We conducted several experiments designed to test whether genetic variation in populations of the crustacean, Daphnia magna, influences the infection dynamics of microsporidian parasites. Genetically mixed experimental populations (ten clones) had similar infection prevalences as single clone populations when exposed to a single strain of each of four parasite species. In a second experiment, we exposed experimental populations to all combinations of four strains of the parasite, Ordospora colligata. Here, parasite prevalence increased with number of parasite strains. Mixed host populations had lower parasite prevalence when exposed to two parasite strains but not when exposed to one, three, or all strains. These results indicate that both parasite and host genetic diversity contribute to disease dynamics.