In Roman times, the island was named Planasia (plain) because of its flatness – its highest point stands at 29 m (95 ft) above sea level.

Pianosa is the fifth biggest island of the Tuscan Archipelago and the only one to be formed out of sedimentary rock of the Neogene and Quaternary; such fossils as echinoderms, mollusca and bryozoa of the Pliocene are frequently found.

[1] The vegetation consists mainly of Mediterranean species as lentisco, fennel, juniper, rosemary and Pinus halepensis, which was introduced on the island in the 1900s.

The animals living on the island are largely small mammals, such as hedgehog and hare, introduced in the 1800s, as well as the pheasant and the red-legged partridge; the magpie and the Audouin's gull nest along the coast and are protected by the National Park.

The Appianos sold Pisa to Gian Galeazzo Visconti in 1399 and established the small Principality of Piombino, which included Suvereto, Scarlino, Vignale, Populonia and the islands of Elba, Montecristo and Pianosa.

On August 15, 1552, the Holy Roman Emperor Charles V of Spain consigned to Cosimo I de' Medici the Principality of Piombino in exchange of a loan of 200,000 scudi.

[5] Pianosa underwent numerous incursions by pirates; the worst took place in 1553, when a French Turkish fleet commanded by Dragut wiped out the population.

Napoleon went to Pianosa from Elba twice, rebuilt the tower, set up a garrison to defend the island, and built some houses to settle farmers.

Although 18th-century documents report that it was once densely wooded, humans and the animals they brought have destroyed the trees on the island, which is now largely grassland except some coastal areas.

[7] In 1856, Leopold II, Grand Duke of Tuscany established a penal colony in Pianosa because it was considered a perfect place to isolate, segregate, and oversee detainees.

A Carabinieri station was established, as was a detachment of Guardia di Finanza, and houses were built to accommodate the families of the soldiers.

The murder of judges Giovanni Falcone and Paolo Borsellino in 1992 led to the reopening of the Agrippa Branch under the 41-bis regime and during the night of July 20, fifty-five Mafia bosses incarcerated at Palermo Ucciardone prison, among them Michele Greco, were transferred by military transport aircraft to Pisa Airport and then to Pianosa by helicopter.

Prior to that time Pianosa had hosted Mafia bosses such as Pippo Calò, Nitto Santapaola and Giovanni Brusca, and had become well known for the brutality inflicted on the prisoners.

Joseph Heller's absurdist anti-war novel Catch-22 is set mostly on Pianosa, at a fictional United States Army Air Forces bomber base during World War II.