Microsporidia are a highly successful and ecologically diverse group of parasites, and thus represent interesting model systems for research on host-parasite interactions. However, such research often requires the ability to cure hosts of infections, a difficult task, given the short lifespan of most invertebrates and the efficient vertical transmission of some parasites. To our knowledge, few treatments are available to cure microsporidiosis in invertebrate hosts, and protocols have not yet been developed to inhibit vertical transmission and thereby cure host lines. We present a protocol for inhibiting vertical transmission of the microsporidian parasite Octosporea bayeri in the freshwater crustacean Daphnia magna. We used 100 mg/L Fumidil B dissolved in the culture medium of the host. This technique allowed Daphnia to survive and reproduce and inhibited vertical transmission of the parasite. The method presented here may be of general interest for other aquatic host-parasite systems involving microsporidia.