Although freshwater ostracod crustaceans show an exceptionally high incidence of transitions from sexual reproduction to parthenogenesis, no prior studies have examined genetic relationships among congeneric species showing breeding system variation. The present study addresses this gap by examining patterns of allozyme diversity among three unisexual and three sexual species in the genus Cypricercus from 46 North American sites. Patterns of genetic relatedness among these taxa suggest that parthenogenesis has evolved on at least three occasions within the genus, and that one all-female taxon is closely related to a sexual species. One unisexual, C. reticulatus, showed very high clonal diversity with many polyploids as well as an allelic array suggesting that much of its diversity originated through interbreeding with sexual relatives. The other unisexuals showed both lower clonal and allelic diversity, but the prevalence of triploid clones suggested that variation might originate from hybridization between diploid asexuals and males of relict sexual populations. The prevalence of multiple X-Y sex determination systems in the ostracods may explain the marked variation in chromosome numbers evident among polyploids. This study suggests that the success of unisexuals may be linked to their ability to recruit clonal diversity through interbreeding with close sexual relatives.