The largest extant New Zealand gecko, Hoplodactylus duvaucelii (Duvaucel's Gecko), is a nocturnal, viviparous species of conservation concern. Hoplodactylus duvaucelii, once widespread throughout New Zealand, is now confined to offshore islands, the majority of which are free from all introduced mammalian predators (mice, rats, cats, mustelids, brushtail possums). A single H. duvaucelii, caught within a fenced reserve on North Island in 2010 was genotyped to determine whether it represents a recent introduction or a previously unknown native relict population. Genotypes from seven nuclear loci and a minimum spanning network of mtDNA haplotypes revealed two clusters representing southern (Cook Strait) and northern island populations. This genetic structure is concordant with variation between these two groups observed in body size, color pattern, and scalation. The mainland specimen was found to possess a mixture of morphological character states typical of northern and southern island populations. Although the individual possessed a unique mitochondrial haplotype, high heterozygosity, and a private nuclear allele, it was no more genetically distinct than conspecifics from isolated island populations. Comparisons with live captive geckos failed to provide evidence that the aberrant specimen represented a recent translocation. We infer that H. duvaucelii has survived naturally on North Island at very low population densities since the human-mediated introduction of novel predators 800 years ago. Our findings suggest a novel conservation priority, which should be prioritized for additional study in the immediate future.