The western population of the skinks number in the "tens" and conservation efforts have been limited by the rugged terrain of their home.
Small numbers of the skinks have been relocated to the predator-proof enclosure at Macraes in an effort to provide a future for the small, genetically different populations.
The eastern populations of the skinks are increasing under the Department of Conservation's programmes at Macraes so the focus is now on the western population.
Grand and Otago skink recovery programme manager with Doc, Andy Hutcheon, said that, until recently, the programme had no way of knowing how closely related the skinks they were breeding were, so there was greater danger of inbreeding.
"If we act now, we can still conserve the genetics of these rare animals."
It was important the genetic lineage of the western population was safeguarded through the captive programme because, given the small number surviving in the wild, there was always the danger of a catastrophic event wiping them out.
"They're on the brink. Maybe they'll hold on, maybe they won't."
It was timely that Karen Ludwig, who worked on the kakapo programme that used a genetic breeding programme to develop the population, had joined the skink programme, he said.
The work built on DNA research done by Landcare New Zealand and the University of Otago's zoology department was deciphering the genetic code.
"From the DNA, we know for certain animals are closely related, but can't say if they are brother and sister."
It was hoped the information would enable the programme to get a representation of all the genetic variety in the west and use that as a base to grow the population in captivity without the risks inbreeding caused in future generations.
"In the short term, it is a lifeboat, breeding up a robust, genetically sound population."
The ultimate aim was to release them back into the wild in a protected place. With the way technology was developing, that might one day be possible, Mr Hutcheon said.
