The Department of Conservation (Doc) has detected a new population of the endangered fish species using environmental DNA sampling.
Doc river ranger Chris Kavasos said Central Otago was home to numerous flathead species found nowhere else in the world.
"It’s amazing to discover a new population," he said.
"Now it’s on us to ensure it survives."
Clutha flatheads are difficult to spot as they camouflage with gravels and cobbles in waterways, so taking DNA samples of the water made for a more accurate survey, he said.
Mr Kavasos and his team detected the presence of Clutha flatheads in Tyre Gully in late 2021 and estimated its population to be in the hundreds.
"It turned out a small waterfall was the only thing stopping trout downstream from migrating up and predating the flatheads," he said.
Clutha flatheads are one of the most endangered galaxias because of trout predation and habitat loss, he said.
He said future flood events could make the waterfall useless as a trout barrier, meaning we could lose the entire Tyre Gully flathead population overnight.
"The removal of trout downstream is already underway and will offer better protection for the population in the long term," he said.
WAI Wānaka, a driving force behind freshwater restoration efforts in the Cardrona Valley, have collaborated with Otago Polytechnic on an adjustable fish passage barrier currently in use at Tyre Gully.
"All this work will increase the habitat available to flatheads, allowing re-occupation of habitats lost through trout predation.
"By removing introduced species, Clutha flatheads are given a fighting chance to survive and even thrive," Mr Kavasos said.
