The Endeavour has a prominent place in Australian history. The ship became the first European vessel to reach the East Coast in 1770 and was scuttled in the harbour as part of the American War of Independence in 1788.
ANMM director and CEO Kevin Sumption said the confirmation was "significant".
"I am satisfied that this is the final resting place of one of the most important and contentious vessels in Australia's maritime history," he said.
The Endeavour, as we know it, was initially launched in 1764 as the 'Earl of Pembroke'.
It was then renamed Endeavour by Britain's Royal Navy four years later.
Over the next three years, the ship voyaged to the South Pacific. Firstly on an astronomical mission to record the transit of Venus in Tahiti before charting Australia's east coast and the coast of New Zealand in 1770.
The vessel lay forgotten for more than two centuries after it was sold to private owners and deliberately sunk in 1778 by British forces.
Today, only 15 per cent of the vessel remains. As such, efforts are now focused on protecting and preserving it.
To mark the occasion of finding and confirming the vessel as The Endeavour, an interactive website has also been launched.
**Since the time of posting, the U.S project's lead investigator has stated that they believe the ANMM have prematurely declared the wreckage to be The Endeavour.