The invasive freshwater algae didymo has been confirmed in Fiordland's Large Burn valley, the first time it has been found in a river west of the main divide.
It was a hugely disappointing result in the battle to keep Fiordland didymo-free, the Department of Conservation said.
Fish & Game field officer Bill Jarvie said the Large Burn, which drained into Caswell Sound, was infrequently visited by fishing and hunting parties.
"We're at loss to know how didymo got here, given anglers are strictly required to obtain a 'Clean Gear Certificate' before entering Fiordland to fish."
The positive didymo sample was the first in Fiordland since 2010 when it was discovered in the lower reaches of the Iris Burn River.
Western Fiordland remained one of the "last frontiers" of rivers to remain free of didymo in the South Island, despite being close to the Waiau River, where didymo was first discovered in 2004.
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