Cook commanded the ship from 1768 to 1771 on his famous voyage mapping the uncharted waters of the south Pacific Ocean, but for years its whereabouts have remained a mystery.
After exploring far-flung lands the boat passed through a number of different hands before it was renamed the Lord Sandwich and used in America's revolutionary war.
"Lord Sandwich was the first lord of the admiralty at the time so the name makes sense -- a nod by its private owner," Dr Kathy Abbass, the executive director of Rhode Island Marine Archaeology Project, a not-for-profit organization set up in 1992 set up to study the area's maritime history, told CNN
"We know from its size, dimension and these records that the Sandwich was the Endeavour."
Now the Rhode Island Marine Archeology Project
(RIMP) says it has managed to identify the wreckage of the Lord Sandwich in Newport harbor, off the state of Rhode Island.
Sent to blockade the city
The organization says the ship was scuttled there by British forces in the lead up to the 1778 Battle of Rhode Island.
"The American army was assembled on the mainland and the French sent a fleet to help," says Abbass.
"The British knew they were at great risk so they ordered 13 ships out to be scuttled in a line to blockade the city. They were sunk in fairly shallow waters."
They now believe this particular piece of history lies on the seabed alongside the 12 other vessels that made up the fleet.
According to RIMP, the wreckages are spread across nine different sites, and "one group of 5 ships includes the Lord Sandwich transport, formerly Captain James Cook's Endeavour."
The group now plans a more detailed exploration of the site and "a more intense study of each vessel's structure and its related artifacts."
One of the most famous ships in naval history, the HMS Endeavour was the boat on which Captain James Cook achieved the first recorded European contact with the east coast of Australia, Hawaii, and the first circumnavigation of New Zealand.
Cook also provided the first accurate map of the Pacific and is believed to have shaped the world map more than any other explorer in history.