The gully is the focus of attention of the project, an initiative between Southern Discoveries, the Fiordland Conservation Trust and the Department of Conservation.
In the 1970s, Sinbad Gully was home to the last known kakapo living on the mainland.
Since then, new species of gecko and skink have been discovered there, some clinging to rock ledges 1600m above sea-level, with frost damage to their bodies.
Doc Te Anau area manager Reg Kemper said something was "obviously wrong" when lizards only survived that high in Fiordland.
The Sinbad Gully Pest Control Project will see Southern Discoveries make a "substantial" annual donation to establish a pest control programme that will allow the threatened birds, lizards and invertebrate species to increase in number.
Controlling possums and stoats would be the key focus for the project.
They were pests which had a "serious impact" on native wildlife through direct predation and competition for food.
In time, if funding allowed, rodent and deer control may also become a focus in the Sinbad.
Once the initial knockdown of possums and stoats had been achieved, ongoing control work would be required to maintain low predator densities.
Maintenance control would be achieved through regular servicing of stoat traps and by monitoring possum densities and controlling as required.
The valley walls surrounding the Sinbad Gully formed a natural barrier that would limit the reinvasion of introduced predators.
Fiordland Conservation Trust chairman Roger McNaughton said the project would not have been possible without Southern Discoveries' "significant donation" - a sponsorship which Southern Discoveries general manager John Robson said was a long-term commitment.
"We are really excited to support such a worthwhile project in this beautiful area of New Zealand.
"This will create a new safe site where threatened species may be reintroduced in the future.
"The Sinbad Gully has all the makings of a spectacular and unique conservation project."
The company planned to profile the Sinbad Gully Pest Control Project in its interpretation material for tourists in the Milford Sound area, including its tour boats, the Milford Sound Discovery Centre and the Blue Duck Cafe.
The educational spin-offs were expected to be far-reaching within New Zealand, and also internationally, Mr Robson said.
