Ciliates control their sexual phenomenon of conjugation (or mating) through a genetic mechanism of mating types, which may either be only two within a species (recalling the duality of sexes in animals), or multiple (recalling self/non-self compatibility systems in plants and fungi). The nearly one hundred species of the most ubiquitously distributed ciliate, Euplotes, all evolved multiple mating types. Based on analyses of Mendelian genetics, these mating types have for long been assumed to be determined by multi-allelic series of genes inherited at a single genetic locus (i.e., the mating-type or mat locus) and responsible for the synthesis of mating type-pecific signaling proteins. The chemical characterization of these signaling proteins (known as pheromones) from an array of Euplotes species has now permitted us to evolve in the study of Euplotes mating types from an approach of Mendelian genetics to an approach of molecular genetics. In this new experimental context, we have cloned and characterized structurally the pheromone (mating-type) gene families of Euplotes species that take different positions in the phylogenetic tree of the genus Euplotes. It appeared that, in accord with the prediction of the Mendelian genetics, early branching species (e.g., E. polaris, E. raikovi and E. nobilii) inherit their mating types at a single multi-allelic locus. However, in disagreement with the prediction of the Mendelian genetics, late branching species (e.g., E. crassus and E. focardii) inherit their mating types at two distinct loci that are likely the result of an event of gene duplication in the germinal (micronuclear) genome. One locus appears to be structurally and functionally homologous with the multi-allelic locus of the early branching species, while the second locus appears to be structurally homologous but functionally divergent.