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Department of Conservation operations director southern South Island Aaron Fleming has described it as a globally significant area.
It was high in biodiversity and home to many special species such as black coral and soft corals like sea pens.
"Uniquely, in the fiords these species can be found at diveable depths due to a phenomenon called deep sea emergence."
While the impact of undaria spreading is unknown, the pest species of seaweed could upset the balance of the ecosystems and species, he said.
"Although many of these species are found potentially deeper than undaria will thrive, the shallow subtidal is also home to a high diversity of invertebrate species such as sponges, ascidians, bryozoans and commercially important species like paua and kina.
"One of the things that Fiordland is renowned for both above and below the water is its pristine nature. The proliferation of a well-known marine pest such as undaria could very well threaten that image."
Environment Southland (ES) biosecurity and biodiversity operations manager Ali Meade said it was difficult to control once it was established in an area.
"Our best defence is to slow the spread of undaria to other areas. The ongoing control of undaria is essential. If left, it could have substantial impacts on the environmental, economic, cultural, recreational and aesthetic values of Fiordland."