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Abstract
We analysed the genetic structure of five populations of Heterocypris from small temporary ponds on the islands of Lampedusa and Linosa (Isole Pelagie, South of Sicily) where we have observed two different adult females morphotypes. The most genetically‐differentiated population, Cavallo Bianco, is made up by females only showing a morphology typical of H. incongruens. All other populations, from both islands, are bisexual and their adult females present a lobe‐like expansion of the selvage (lamella hyalina) on the posterior margin of the left valve. In one locality, Vallone della Forbice, both female morphotypes occur. The analyses of individuals raised in the laboratory microcosms confirmed the genetic differentiation between morphotypes and their different reproductive modes. The adult females without a lamella hyalina are apomictic, whereas females with this feature are am‐phimictic. Genetic differentiation of the two female morphotypes is compatible with the hypothesis that the two morphotypes represent different species of Heterocypris although, such a morphological differentiation is not unusual in populations of the same parthenogenetic species, and we found evidence of hybridisation between males and parthenogenetic females.