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The wingless Maungatua stonefly, just under 2cm in length, was found in inhospitable country just below the summit of Mt Maungatua, which overlooks Dunedin airport.
University of Otago zoology professor Jon Waters was up on the mountain about two years ago looking for other things when he discovered a chunky stonefly beneath a rock that "didn't look like anything else we'd ever seen", leading his team to conduct DNA analysis of the insect.
Juvenile stoneflies or nymphs were found at first, and later a larger nymph was caught by researchers and reared to adulthood to study.
The study, and formal description of the new species, which was led by PhD student Brodie Foster, is now complete.
The stoneflies are thought to have flown or been blown over to the mountain range before gradually losing their wings due to the cold climate and high winds, and are believed to have been isolated for about 2 million years.
"This would rank right up there in terms of my research career, to just find something sitting in one spot," Prof Waters said.
"The next step is we've found it only in two streams at the moment. We really want to nail down its [habitat] up there.
"It may be that we've already found all the [individual Maungatua stoneflies] there are," he said.
"The track's about non-existent; it's pretty full-on. It's not the easiest place to look for these guys."
The length of time the stonefly had been isolated helped explain why it was so distinctive, he said. There was a very good chance the insect would never have been discovered at all.
The teams' research on alpine insects was funded by a Marsden grant.
Most stoneflies can fly, developing large wings once they emerge from streams as adults - but a handful of New Zealand species have evolved to lose them.
Mr Foster said the discovery would contribute to his studies of wing reduction in stoneflies.