The Fiordland Marine Guardians is concerned that native seaweeds and shellfish in Fiordland could be displaced by a seaweed pest.
A specimen of Japanese undaria kelp has been found on a barge at Sunday Cove in Breaksea Sound.
Undaria has spread along much of the east coast of New Zealand since the 1980s.
It's the first time undaria has been found in Fiordland.
Fiordland Guardians chairman Malcolm Lawson says undaria spreads rapidly and can upset the ecosystem.
MAF Biosecurity, Southland Regional Council and the Department of Conservation will investigate whether it has spread to other parts of Fiordland.