John was born in Amathus on Cyprus c. 550 to the patrician Epiphanius, a governor of the island. He married and had children, but was a widower when he was called to become patriarch of Alexandria on the recommendation of his friend, the city's imperial prefect Nicetas. The Chalcedonian see of Alexandria had been vacant since the death in 609 of Theodore during the capture of the city by Nicetas. In 611 John assumed the throne, becoming the fifth Chalcedonian bishop of Alexandria to bear that name.