Lepidodactylus lugubris, often cited as an exception to the rule that vertebrate parthenogenetic species must arise via hybridization of two sexual species, is shown to be of hybrid origin. Using karyotypes, sequences of the cytochrome-b gene, and protein electrophoresis we have shown that the maternal ancestor is the recently rediscovered species L. moestus from Micronesia; the paternal ancestor is an undescribed species whose range extends from French Polynesia to the Marshall Islands. Lack of sequence divergence between some individuals of L. lugubris and L. moestus suggests that independent clone production through hybridization of the sexual ancestors is probably recent, ongoing and has occurred several times. The only known location where both parental species and L. lugubris are sympatric is Arno Atoll (Marshall Islands). Field and museum surveys of over 10000 individual geckos establish that previously reported sexual populations of L. lugubris are misidentified and in fact are either the sexual parental species, other undescribed sexual species, or rare developmentally abnormal males.