It was Cosimo I de' Medici’s idea to build a shipyard in Pisa for the vessels of the powerful Tuscan fleet. It was part of a wider scheme to restore Pisa to its ancient splendour, after its fall into disrepair following surrender to Florence in 1509.

In 1562 the Order of Knights of St. Stephen was instituted, it too, with the shipyard designed by Buontalenti, was part of this plan. By 1540 it was already fully operative, and in 1546 this new shipyard built by the Medicis launched the first galera to be constructed entirely by local craftsmen.

The shipyard was constructed in eight aisles, each roughly 60 metres long, 8 metres high and 10 metres wide. Soon the yard had to be enlarged. so in 1563 the nearby "Giardino dei Semplici" (medicinal Herb Garden), had to be relocated. However, competition from shipbuilders in Livorno and Portoferraio and changes in maritime policy soon began to cause a slow but inexorable decline until, in mid 18th century, under the rule of the Lorena family, the buildings were adapted into stabling for the horses of the Dragoons regiment.

Now, in the renovated part of the Shipyard buildings, some highly important archaeological finds are on show. These are wrecks and objects of daily use recovered from the ancient Etruscan and Roman port. (5th century BC to 5th century AD) near today’s San Rossore train station. These objects are to become the focal point of the future museum of the Ancient Ships.