A population of kiwi once thought to be thriving in Marlborough is being threatened by inbreeding.

Dr Helen Taylor, an expert in kiwi genetics and inbreeding, analysed a population of the little spotted kiwi on Long Island, and found poor hatching success compared to a Wellington population.

Taylor's research found nearly two-thirds of the 50-strong population were direct offspring of the Queen Charlotte Sound island's founding pair.

She said they expected to find more birds of second, third, and fourth generations.

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"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," she said.

The University of Otago study conducted autopsies of unhatched eggs, finding many had malformed embryos, or none at all.

The Long Island population was thought to be thriving, and Taylor said the study showed population growth alone was not enough to predict how well the kiwi were doing.

"This 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 said.

Previous work by Dr Kristina Ramstad at Victoria University of Wellington showed little spotted kiwi have extremely low genetic variation as a species.

All 1700 existing little spotted kiwi are descended from just five birds that were moved to Kapiti Island in the early 1900s.

Taylor's findings appear in the international journal Molecular Ecology.