In dioecious parasite species, genetic structure can differ between sexes, as recently demonstrated for the digenetic trematode Schistosoma mansoni and the ectoparasitic tick Ixodes ricinus. This article presents some of the methods that allow detecting such a pattern in natural populations. The proximate and ultimate factors that potentially generate a sex-specific genetic structure are discussed, as are evolutionary and epidemiological consequences for dioecious parasites and vectors.