Asexual reproduction in vertebrates is rare and generally considered an evolutionary dead end. Asexuality is often associated with polyploidy, and several hypotheses have been put forward to explain this relationship. So far, it remains unclear whether polyploidization in asexual organisms is a frequent or a rare event. Here we present a field study on the gynogenetic Amazon molly, Poecilia formosa. We used multilocus fingerprints and microsatellites to investigate the genetic diversity in 339 diploid and 55 triploid individuals and in 25 P. mexicana, its sexual host. Although multilocus DNA fingerprints found high clonal diversity in triploids, microsatellites revealed only two very similar clones in the triploids. Phylogenetic analysis of microsatellite data provided evidence for a monophyletic origin of the triploid clones of P. formosa. In addition, shared alleles within the triploid clones between the triploid and diploid genotypes and between asexual and sexual lineages indicate a recent origin of triploid clones in Poecilia formosa.