Differences exist in the population structure of Heterocypris in five temporary ponds on the islands of Lampedusa and Linosa (Isole Pelagie, south of Sicily). In a temporary pond on Lampedusa (Cavallo Bianco) we found only H. incongruens females. All the other populations were bisexual, with the female/male sex ratio varying from 1 to 18. We analysed and measured a sub-sample from each population and observed, as a typical morphological feature of adult females in the bisexual populations, a lobe-like expansion of the selvage (lamella hyalina) on the posterior margin of the left valve. In another temporary pond from Lampedusa (Vallone della Forbice) both females with this lamella and others without it occur. We discuss the possible coexistence of two lineages of H. incongruens each having a different reproductive mode. The parthenogenetic lineage comprises females without a lamella hyalina whereas the bisexual females possess this feature. Alternatively, we hypothesise the sympatry of two different species of Heterocypris: H. incongruens and H. barbara. In this hypothesis, H. incongruens is parthenogenetic and H. barbara is amphimictic. Differences in mean body size between the adult females with and without the lamella hyalina are in accordance with values reported in the literature for niche differentiation among sympatric taxa.