Periods of low host density impose a constraint on parasites with direct transmission, challenging their permanence in the system. The microsporidium Octosporea bayeri faces such constraint in a metapopulation of its host, the cladoceran Daphnia magna, where ponds frequently lose their host population due to ponds drying out in summer and freezing in winter. We conducted experiments aimed to investigate the mechanisms of transmission of O. bayeri, and discuss how these mechanisms could contribute to the parasite's permanence in the system. Spores accumulate in the fat cells and the ovaries of the host, and vary in morphology, possibly corresponding to 3 different spore types. Horizontal transmission occurred through the release of spores from dead hosts, with the proportion of infected hosts depending on the spore dose. Further, spores are able to persist outside the host both in dry and wet conditions. Vertical transmission occurred to both parthenogenetic and sexual offspring. The former were invariably infected, while the sexually produced resting eggs (=ephippia) had a less efficient transmission. The parasite may be carried by the ephippia, and thus disperse to new ponds together with the host. Together, these mechanisms may allow the parasite to endure periods of harsh environmental conditions both outside and inside the host.