Born at Pesaro, Francesco Maria was the son of Guidobaldo II della Rovere, Duke of Urbino, Count of Montefeltro and Vittoria Farnese, Princess of Parma. He was raised between 1565 and 1568 at the Royal court of Philip II of Spain. While there he met a Spanish girl and informed his father of his intention to marry her . But his father would not allow it and demanded he return to Urbino. In 1570 Francesco Maria married Lucrezia d'Este, a daughter of Ercole II d'Este. His father died only a few years later, in 1574, and Francesco Maria succeeded his father as Duke of Urbino.

By 1580 the family estate was in crisis and Francesco Maria was forced to sell his family's titles - the Duchy of Sora and Arce - for 100,000 scudi to Giacomo Boncompagni.

Francesco Maria's marriage, though, remained childless and Francesco Maria needed a male heir. Without one, his family's remaining titles would lapse on his death and his entire estate would be acquired, by default, by the Papal States.

So in 1599, after the death of first wife Lucrezia, he married his cousin Livia della Rovere, 36 years his junior. On 16 May 1605 their long-expected and only child Federico Ubaldo was born.

Federico Ubaldo married Claudia de' Medici in 1621 and was made Duke by his father. However, Federico died in 1623 from an epileptic attack, leaving only a daughter, Vittoria Della Rovere, wife of Ferdinando II de' Medici, Grand Duke of Tuscany; their child was Cosimo III de' Medici, Grand Duke of Tuscany; none of Cosimo III's children had heirs.

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