Iago ab Idwal was king of Gwynedd from 1023 to 1039, but in the latter year he was killed by one of his own men and the throne was seized by Gruffydd ap Llywelyn. Cynan was forced to flee to Ireland and took refuge at the Danish settlement of Dublin. He married Ragnaillt daughter of Olaf of Dublin, son of King Sigtrygg Silkbeard and a member of the Hiberno-Norse dynasty. Ragnaillt, who appears in the list of the fair women of Ireland in the Book of Leinster, was also a descendant of Brian Boru.
Cynan may have died fairly soon after the birth of their son Gruffydd ap Cynan, for the near-contemporary biography of Gruffydd details Cynan's ancestry but does not refer to him in its account of Gruffydd's youth; describing Gruffydd's mother telling him who his father was and what patrimony he could claim. Gruffydd ap Llywelyn was killed in 1063, by his own men according to Brut y Tywysogion. The Ulster Chronicle however states that it was Cynan ap Iago who killed him.
As his son Gruffydd was supposedly born c. 1055, the date of death "1039" is doubtful (Gruffydd died 1137).
Cynan's claim to the throne of Gwynedd was passed on to his son. When Gruffydd first appeared on the scene in Wales the Welsh annals several times refer to him as "grandson of Iago" rather than the more usual "son of Cynan", indicating that his father was little known in Wales.