We investigated the genetic population structure in a metapopulation of the plant Silene latifolia (Caryophyllaceae) and its fungal pathogen Microbotryum violaceum (Ustilaginales), a pollinator-borne disease. Population structure of the host plant was estimated using allozyme markers and that of the fungus by microsatellites. Both host and parasite showed significant differentiation, but parasite populations were 12 times more strongly differentiated than those of the hosts. We found significant isolation by distance for host populations but not for parasite populations. Higher population differentiation for the parasite may result from small effective population size, high selfing rates, or low migration rate. In this system, hosts are obligate outcrossers and they migrate by seeds and pollen, whereas parasites can self-fertilize and migrate only on pollinating insects. We discuss the effect of limited gene flow in this parasite on its coevolutionary interaction with its host, and its potential for local adaptation on sympatric host populations.