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Ferdinand succeeded his father as Grand Duke of Tuscany in 1790, and ruled in Tuscany until 1801, when he was forced by Bonaparte to give up Tuscany to the Bourbons of Parma, who turned it into the Kingdom of Etruria.
Ferdinand was compensated by being given the secularized lands of the Archbishopric of Salzburg and several other ecclesiastical princes in Germany, and was made a Prince-elector of the Holy Roman Emperor.
By the Treaty of Pressburg of 1805, Ferdinand was made to give up Salzburg, which was annexed by his brother, the Emperor of Austria, and instead became Duke of Würzburg, a new state created for him from the old Bishopric of Würzburg.
During the last dreadful period of the war, in 1644 FerdinandIII gave to all rulers of German states the right to conduct their own foreign policy (ius belli ac pacis).
Ferdinand married three times, first to his cousin, the Infanta Maria Anna of Spain, by whom he had two surviving sons: Ferdinand IV, his eldest, who predeceased him, and Leopold, who ultimately succeeded him.
She died in 1649, and Ferdinand married a third time, to Eleonora Gonzaga, daughter of the Duke of Mantua.