The garden was planted in 1511 near a Perthshire castle to mark the completion of the warship, the Great Michael - which was hailed as a marvel of the reign of King James IV and was twice the size of its English contemporary, the Mary Rose.
Chroniclers recorded that the commemorative garden was created in hawthorn to mirror the exact dimensions of the wasrship. But it was destroyed in the 18th century and its location lost to history.
Historian Louise Yeoman rediscovered the site, near Auchterarder in Perthshire, while investigating the ship's history. She found the garden marked the furthest inland point used for gathering great oaks to build the warship.
And it was overlooked by the now-demolished Tullibardine Castle, owned by the Murrays, whose chief carpenter John Drummond was chosen by the king to supervise the great ship's construction.
Dr Yeoman said: "The Great Michael was an incredible feat of ship-building - 1,000 tonnes with four masts and enormous cannons that were used to smash castles from the sea.
"The Fife chronicler Pitscottie claimed in the 16th century that the craftsmen who built the Great Michael were so proud of her they planted out her enormous dimensions in hawthorn.
"This clipped hawthorn garden with an ornamental pond in the shape of the ship, must have been 200ft by 40ft in size.
"It seemed like a fairytale but now, for the first time, we can say it existed, where and why."
Historians believed the garden was located at the land-locked castle of Tullibardine - but were puzzled why the ship was remembered in rural Perthshire, so far from the sea.
Dr Yeoman said: "The Great Michael needed 1,200 of the tallest, straightest oaks, but Scotland was scraping the barrel at this time, especially in the Lowlands.
"Treasurer's accounts record that oak was taken from the woods of Kincardine. People assumed this referred to Kincardine on Forth, but I felt it was impossible as there was no great oak wood there. Some of the last great oak trees were, however, found in the Kincardine Glen, near Tullibardine Castle, precisely because they were so far from the sea.
"The garden they created would have marked around the furthest from the sea that wood came for the Great Michael.
"It would have been hauled from Kincardine Wood down Glendevon to the Forth ports like Alloa, where ships would have taken it to Newhaven, where the ship was built, or the royal dockyards at Pool of Airth."
Dr Yeoman and a team from the Edinburgh Archaeological Field Society pinpointed the exact location of the former castle using geophysics.They were then able to match centuries-old maps to establish the commemorative garden's location.
The Great Michael was the largest warship in Europe when the vessel was launched at Newhaven in 1511 to become the flagship of the Royal Scottish Navy.
She was more than twice the size of the Mary Rose, the pride of the English fleet which launched in 1509, and it was said that "all the woods of Fife" had gone into her construction.
Mons Meg, now one of the main attractions at Edinburgh Castle, is rumoured to have been part of the warship's armament.
Around 240ft long, the vessel was home to 1,000 marines, 300 sailors and 120 gunners. But the vessel was expensive to maintain and, after James IV was killed at the Battle of Flodden in 1513, the Great Michael was sold to King Louis XII of France.
• Great Michael's Afterlife will be broadcast on BBC Radio Scotland on Monday, 6 December, at 3:30pm.