The species is endemic to Stewart Island / Rakiura in the far south of New Zealand, where it was discovered in 1969.

[3] The harlequin gecko has been assessed as Endangered by the IUCN since 2018, owing to its rarity, small range and declining population.

Stewart Island is overrun with invasive predators such as cats (Felis domesticus) and rats (Rattus rattus, R. exulans, and R. norvegicus), which have also contributed to declines among native bird species.

[1] As of 2012 the Department of Conservation (DOC) classified the harlequin gecko as Nationally Vulnerable under the New Zealand Threat Classification System.

[8] The species is protected under Appendix III of the Convention on International Trade in Endangered Species (CITES), meaning international import/export is regulated by the CITES permitting system.