Parthenogenesis, or all-female clonal reproduction, is rare among vertebrates. This is often attributed to the selective disadvantages of assumed reduction of genetic diversity in the absence of sex. However, parthenogenetic vertebrates have highly complex evolutionary histories, with most arising through hybridisation and many being polyploid. Here, we show that geographically widespread triploid parthenogenetic forms of the Australian gekkonid Heteronotia binoei are considerably diverse despite their clonal reproductive mode, with patterns of variation consistent with two previously identified reciprocal hybrid origins and numerous backcrossing events. We also confirm a two-fold increase in genome-wide heterozygosity among parthenogens (10.6%) compared with the sexual progenitors (4.63%). Our SNP-based diversity estimates exceed prior predictions for clonal H. binoei lineages based on karyotype and allozyme data. We also find evidence of repeated and geographically widespread backcrossing in both western and central Australia. This supports the long-standing hypothesis that parthenogens are able to partially recover parental niches by 'freezing' genotypic diversity present within the sexual forms. Understanding how asexual clones attain ecological success has implications for managing both invasive species, many of which are clonal, and threatened species, which often face similar challenges associated with reduced genetic diversity. Overall, our findings demonstrate that sex, historical or ongoing, is instrumental in the persistence of asexual lineages, contributing to a broader understanding of the evolutionary dynamics of parthenogenesis.