The mourning gecko, Lepidodactylus lugubris, is an all-female parthenogenetic species widely distributed in tropical and subtropical regions. We examined clonal diversity of L. lugubris in southern Japan, the northernmost extremity of the species' range. Results indicated that the assemblages of the Ogasawara Islands are composed solely of diploid clone A, which may have originated from artificial transportation after World War II. Assemblages of L. lugubris in the Ryukyu Archipelago were composed solely of triploid clone C. This, along with literature records, suggests that the gecko recently colonized the Ryukyu Archipelago on limited opportunities from limited sources. Samples from the Daito Islands included both diploid and triploid individuals representing one and 11 different clones, respectively. Except for one triploid clone (clone B), these clones were most likely to be endemic to the Daito Islands. Analyses of genotypic pattern suggest that most of the putative endemic triploid clones of the Daito Islands originated from iterative crosses between sympatric diploid clones and males of closely related bisexual species that were most likely extirpated subsequently.