As part of her PhD research at Otago University, Dr Stefanie Grosser analysed ancient DNA from the remains of more than 100 little penguins, including bones dating back to pre-human times and specimens from archaeological deposits and museums.
"Amazingly, all of the bones older than 400 years belong to the native New Zealand species," she said.
Dr Grosser said the arrival apparently followed the decline of the native penguin, which early human settlers and introduced predators hunted.
The Australian species were set apart by a few subtle differences in their colour, body and cranium size.
Other researchers had previously shown that calls differed between Australian and New Zealand little penguins and females preferred the calls of males of their own species.
"You could say the Aussies like hearing 'feesh', while 'fush' sounds better to Kiwi ears," Dr Grosser joked at the time of the December findings.
But how they got here remains a mystery -- and one we might never solve.
"It's one of those unlikely events that they happened to rock up on the Otago coastline and got a foothold," said study leader Professor Jon Waters, of Otago University's Department of Zoology.
"You could make up a story that maybe an Australian ship picked up 10 and brought them over, but I'd find that really hard to believe."
The Australian sub-population appears confined to Otago. DNA analysis from other colonies, such as Wellington, Kaikoura and Banks Peninsula, turned up only the New Zealand lineage.
"It's possible we might find another colony of Aussies somewhere like Fiordland, we don't know."
Professor Waters believed the findings should bring about a different approach to the species' conservation.
"We have to think about them as being not one thing, but two, and manage them separately -- so there might be a real paradigm shift."
The native penguin, which on average stands at just 25cm and weighs 1kg, is considered in decline in New Zealand. Dogs pose their greatest threat.
The research, supported by the Marsden Fund and the now-closed Allan Wilson Centre, also provides the latest example of penguins winding up on foreign shores far from home.
Little blue penguins have been found as far as Patagonia in South America.
Other famous penguin stories have included the Antarctic emperor penguin Happy Feet, which captured Kiwi hearts after it arrived in Kapiti in 2011, and Katrina, a Fiordland penguin that swam 3000km to Mt Gambier, South Australia, in 2013.
How DNA has redefined our native species
The yellow-eyed penguin
DNA analysis and carbon-dating led to findings published last year that revealed a change-over between the yellow-eyed penguin and another penguin species that became extinct around the same time as the moa.
An Otago University team showed the waitaha, which was slightly smaller than the yellow-eyed penguin, vanished within 200 years of Polynesian settlement of New Zealand, before 1500AD.
In one of the most rapid biological transition events documented, the yellow-eyed penguin, or hoiho -- considered one of the world's rarest penguin species with a population of between 6000 and 7000 -- moved to the mainland from the subantarctic islands and replaced the waitaha within just a few decades, in the early 1500s.
The New Zealand sea lion
That research had fascinating parallels with the fate of a pre-historic species of New Zealand sea lion, which once dominated South Island shores before they became extinct as recently as between 1300 and 1500AD, soon after Polynesian settlement.
DNA analysis reported in 2014 showed their place on the New Zealand mainland was quickly taken by today's modern population, which was previously limited to the cold waters of the subantarctic.
The kiwi
2014 was also the year that scientists corrected the shocking suggestion that our national bird arrived here when its winged ancestor flew in from Australia.
The 150-year-old mystery was finally solved by DNA sequencing that revealed the bird was more closely related to the extinct, 2.3m tall elephant bird, a native of Madagascar.
The moa
A separate study in 2014 put even more genetic distance between the extinct moa and their old bush mates, the kiwi.
DNA-based research led by New Zealand scientist Professor Allan Baker suggested the giant birds were more closely related to a flying South American bird still alive today than our national icon.
The South American tinamous, one of the world's most ancient living groups of bird, can fly and are not categorised as ratites, but are considered close relatives because of the shared structure of their palate bones.
