The villa, initially the country house of Baron Giorgio Andrea Des Geneys, was built in the early 1800s on a promontory of the island of La Maddalena. The baron bought a plot of land in Padule from a certain 'patron Francesco Santucci' in the western part of the island, with a vineyard of more than 4,000 vines, a vegetable garden, and enclosures for livestock; he then bought two small neighbouring plots. On the Baron’s death, the villa was sold to a wandering Englishman, Sir Hyde Parker, and from there to another Englishman, James Phillips Webber, whose presence on the island dates back to 1851.
Webber, after which the villa was named, was the eldest of three children born to Edward Webber, a British army officer. His mother was Charlotte Margaret Phillipse, a member of a Dutch high-ranking family who settled in New York but fled to England due to the American War of Independence. In 1822, James Webber emigrated to Australia as a settler. He acquired a significant land grant near Newcastle, on which he cultivated tobacco, cotton, and vineyard crops. He also held important public offices during his time there. In 1836, he returned to Europe after selling his property and earning £4,814.
Webber passed away in 1877 in Pisa and bequeathed his estate to Maria Tamponi, wife of Webber's adopted son Luigi Alfonso Russo Webber, along with their four children. Following Maria's passing in 1928, the heirs were unable to sell the villa.
In 1943, the Italian Royal State requisitioned the villa to detain the prisoner Benito Mussolini, who had been defied by the Grand Council and arrested on the king's orders.
In later years, the villa was abandoned. At the current time, the building is in a poor state of preservation, although it retains much of its original finish. The most valuable removable architectural elements, such as the fireplaces, have been stolen, although there are still elements of great value, such as the flooring, some painted ceilings, some original fixtures, the banisters and railings of a decorated wrought-iron staircase.