The excavations in Stabiae begun on 7th June 1749 by order of Charles III of Spain (House of Bourbon). An urban structure on the Varano plateau was excavated, revealing shops, streets, and six residential villas. As was the custom at that time, the excavation involved the digging of a series of small tunnels, subsequently reburied, to begin excavation elsewhere, when the findings were not deemed worthy of being displayed in the Bourbon Museum in Portici The excavation, conducted by two engineers, the Spanish Alcubierre and the Swiss Carl Weber, started from Villa San Marco (1749-1754), then moved to the Villa of the Shepherd (1754) and Villa Arianna, also including the adjoining complex (1757-1762).

After a pause of about thirteen years, the excavation was resumed in 1775 in the area of Villa Arianna and some other Stabian rustic villas.
The work produced by the Bourbon archaeologists was published in 1881 by M. Ruggiero, an architect and collaborator of Fiorelli, the then director of the excavations in Pompeii. The entire Bourbon documentation, consisting of excavation logs, drawings and graphs, was collected. A plan of the overall findings in the Stabiae area was drawn up as well. In the 50s, there was a new surge of interest for Stabiae, and the final excavation of the villas was conducted by L. D’Orsi. For preservation and conservation reasons, many frescoes were detached from the walls of the villas and collected in the Antiquarium, opened in 1957.