Understanding the source and diversity of clones is necessary to resolve the complicated issues surrounding the apparent evolutionary stability of sexual reproduction. The source of clones is important because present theory is based on an “all else equal” assumption, which is predicated on the idea that clonal mutants are derived from and compete with local sexual populations. Clonal diversity is important because it reduces the advantage of sexual reproduction under either soft selection (the Tangled Bank Hypothesis) or under strict frequency-dependent selection (the Red Queen Hypothesis). In the present study, protein electrophoresis was used to determine the source and diversity of clones in a freshwater snail (Potamopyrgus antipodarum) in four glacial lakes in which sexual and clonal females were thought to coexist. The results showed (1) that the populations were mixtures of diploid sexual and triploid asexual individuals, (2) that genotypic diversity of clonal populations is very high in all four lakes (but lower than in the sympatric sexual populations), and (3) that the clones are polyphyletically derived from their sympatric sexual populations. Consequently, repeated mutation to parthenogenetic reproduction since the Pleistocene has introduced a different and diverse set of clones in all four lakes. Such diversity may provide a challenge for the ecological theories of sex that rely on frequency-dependent selection.