Several hypotheses were proposed to account for geographic parthenogenesis that is the disjointed distribution of a species' sexual and asexual forms. In the areas affected by glaciations the parthenogenetic forms would have had ecological success and hybridization and polyploidy would have been the driving forces in their success. Limnocythere inopinata is well-represented in Quaternary non-marine sequences and is useful for studying the evolution of geographic parthenogenesis. We analysed the genetic variability of twelve populations from sub alpine Italian lakes, Austrian lakes and a pond, in an area that was covered by ice during the Pleistocene. In all samples we found only parthenogenetic females. Using allozymes, we described at least 33 different clonal lineages in the total of 812 females. We found no evidence for polyploidy. Clonal diversity is relatively high and may reflect the genetic diversity of ancestral sexual metapopulations. In L. inopinata, geographical parthenogenesis seems the result of historical and ecological factors and is not linked to polyploidy and hybrid advantage.