Cynan was the son of Iago ab Idwal ap Meurig, king of Gwynedd. He was forced to flee to Ireland when his father was killed in 1039 and replaced by Llywelyn ap Seisyll's son Gruffydd ap Llywelyn. Cynan took refuge at the Danish settlement of Dublin, and there he married Radnailt of Dublin, daughter of Amlaib mac Sitric, heir of Dublin, son of Sitric of the Silken Beard, (Norse) king of Dublin and a member of the Hiberno-Norse dynasty. Radnailt, whose mother was Máelcorse ingen Dúnlaing, appears in the list of the fair women of Ireland in the Book of Leinster. She was a descendant of Brian Bóruma mac Cennétig, king of Ireland.
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; it describes 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._ However the Ulster Chronicle states that it was Cynan ap Iago who killed him, which would indicate that Cynan died on or after 1063.
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.