After the death of his first wife Marguerite Yolande of Savoy, Ranuccio II married in 1663 his cousin Isabella. But the couple only met on 18 February 1664, when Isabella arrived in Parma. For this occasion, a grandiose celebration and musical spectacles were organised. The couple had three children, all of whom would survive childhood. Only the youngest Odoardo, would have issue; he was the father of Elisabeth Farnese, queen of Spain and ancestor of most modern royalty.
But the birth of her son proved fatal to Isabella, who died of complications nine days later on 21 August, at Colorno. She was buried at the Sanctuary of Santa Maria della Steccata in the city of Parma on the 23 August. Her husband remarried in October 1668 to her sister Maria d'Este. By her he had a further seven children as well as the last two FarneseDukes of Parma.