An inbred population of little spotted kiwi population on a Marlborough island is raising questions about how conservationists monitor the health of threatened species.

A new study from Otago University, published in international journal Molecular Ecology, reveals the country's second-rarest kiwi species is feeling the "silent effects" of a small gene pool.

Dr Helen Taylor and her colleagues say their findings show the problem of relying on population growth to determine the group's health.

They analysed the genetic diversity of two of 10 established populations: on Long Island and at Wellington predator-free ecosanctuary Zealandia.

In the 1980s, two of the little spotted kiwi were moved to Long Island and since then, nearly two thirds of the 50-strong population can trace direct lineage to the founding pair.

Dr Taylor says she'd expect the majority of that population would be second, third or fourth generation offspring.

Little spotted kiwis can live up to 80, with around 1700 of the birds on predator-free islands and fenced sanctuaries.

"The overabundance of first-generation birds suggests that the damaging genetic effects of inbreeding are strongly affecting hatching, survival and possibly reproduction of the subsequent generations."

The island's birds have a poor hatching success compared to those at Zealandia, whose population was founded with 40 kiwi, but it's not for lack of trying.

The study showed the Long Island birds made "greater efforts" to reproduce, sometimes having more than one egg per clutch and sometimes incubating two clutches a season.

Autopsies on abandoned or unhatched eggs revealed a multitude of problems, including no detectable embryo development, malformed embryos or chicks wrongly positioned for hatching.

Dr Taylor says the Long Island's kiwi population is in trouble.

"This little spotted kiwi population is struggling to grow past the first generation. Once the original pair of kiwi die or become too old to breed, the population will likely go into decline," she says.

Previous studies from Victoria University have shown exceptionally low genetic diversity in little spotted kiwi with the 1700 population descended from just five birds moved to Kapiti Island in the early 1900s.

Dr Taylor says the findings could apply to other threatened species whose populations are being grown from a small founding group.

"Just because a population appears to be growing does mean it is secure in the long term. We could never have worked out what was happening in the little spotted kiwi on Long Island without genetic data."

The Department of Conservation (DOC) manages the birds, which are moved between populations to minimise loss of genetic diversity.

The study had financial backing from the Government as well as from Victoria University, Centre for Biodiversity and Restoration Ecology, Allan Wilson Centre, DOC and the Kaitiaki o Kapiti Trust.

Newshub.