"This is the sort of thing we're up against," says biodiversity ranger John Neilsen, who was incredulous when told the stoat had similar DNA to specimens from the Waitakeres, 45km away.
Rangitoto, which is joined to Motutapu by a causeway, is a rat's paradise. Its 600-year-old volcanic rock is honeycombed and covered in shrub. It contains a million hiding-spaces.
Motutapu is millions of years old and made up of gentle hills and wide open spaces.
In August, the two islands were declared pest-free - this time with confidence - after an eradication programme which attracted some controversy for its heavy use of poisons - up to 16kg of brodafacoum a hectare.
Last month the Herald visited Motutapu to see how the introduction of the endangered birds tieke (saddleback) and takahe had fared.
Tieke are a noisy, playful species, well-suited to translocations, says DoC ranger Hazel Speed. She plays a recording of a tieke birdcall near the spot they were released, and within a minute two of the birds fly into the branches above our heads.
Ms Speed and her colleague's devotion to the birds' survival is intense.
They talk of their "hot gossip sessions" about the tieke, when they compare every nuanced relationship between the birds, every romance and divorce, and every mood swing.
At last count, all 20 tieke were accounted for at Motutapu - a remarkable result which reflects New Zealand's world-leading techniques in translocation.
The true test will be keeping that number for a year after the translocation. Ms Speed says 14 out of 20 would be a great survival rate.
To Ms Speed's delight, the endangered birds have also bred 16 chicks since arriving in August.
There is more uncertainty about the takahe, of which only 250 remain.
The flightless, short-legged, blue and green birds disappeared in the early twentieth century, and were thought to be extinct, until they were rediscovered in Fiordland in 1948.
Four takahe were released in August, but more birds will need to be introduced before a population can be established at Motutapu.
Because of their precious status, the slightest inkling that a rodent has reached the island will set off a full-scale pest response. Mr Neilsen sets a minefield of traps around the spot the rat, mouse or cat was last sighted, and brings a specially-trained dog to the island.
He said one of the biggest obstacles to robust pest control was mischievous visitors who set off traps - up to 20 at a time.
"The traps are 200m apart, so you can imagine the gap in the trap line."
The conservation effort is two-tiered. DoC focuses primarily on pest control, while the Motutapu Restoration Trust battles the choking weeds on the island and plants native trees.
On the day the Herald visited, volunteer co-ordinator Bridget Vercoe was taking a group to weed out mothplant on Motutapu.
"This used to be called shit gully," she told the volunteers, pointing to the most forested valley on the island.
"In 2002, we would look down on this valley and it was just dripping with vines."
Native trees are now breaking free of the clasp of climbing weeds, and tieke were spotted in their branches earlier in the month - a tangible stamp of approval for the trust's efforts.
As we board the ferry home, I ask Ms Speed whether it is a pipe-dream to rescue the populations of birds many New Zealanders have never heard of. She responds without missing a beat.
"We've destroyed the wild, and we'll not get it back. But every species we bring back helps.
"Until recently this birdsong wasn't heard here. So, to hear it is a fantastic thing."
