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The area has been inhabited since the seventh century BC as evidenced by the graves found in the Valle Cappellana area. The town is located on the site of a large Roman villa in the countryside, near the Via Clodia and the Via Cassia, which dates it back to the III-IV century AD. The villa had spas, swimming pool, stables and barns.

The area was then quickly abandoned during the period of the invasion and the most disastrous raids were those of King Liutprand of the Lombards and Frederick II.

The area was repopulated in the sixteenth century when Pope Leo X granted the fiefdom to Lorenzo Anguillara of Ceri who passed it to his son Giovanni.

The name of San Giovanni came from the feudal lord who in 1550 supported the arrival on site of some twenty settlers, who came from various parts of Italy to populate and cultivate the land, thanks to numerous privileges and concessions.

When the Ceri family died, Pope Pius II granted the fiefdom to the Apostolic Chamber that leased its lands.