Cosimo I started having the Dome in Portoferraio built in 1548, the same time the Medicean walls were started; it was consacrated in 1554 and dedicated to the Nativity of the Blessed Virgin Mary.
In the beginning it only had one nave but was made bigger over the centuries. The Works on Parish Churches was established under the French rule (and their first worker was the famous Giuseppe Ninci). On this occasion marble from the Church of Carmine, deconsacrated years before by Napoleon l who had it turned into a Theatre, was used to replace the high altar made of plaster.
The Confraternita della Reverenda Misericordia was founded in 1566 near the altar of the wooden crucifix from the year 500, at that time on the right of the High Altar. On May 4th 1814 a Te Deum was held before Napoleon Bonaparte who had just been nominated sovereign of the Island of Elba.