Philip O'Reilly married Rose O'Neill, the sister of Owen Roe O'Neill, the military leader of the Irish in Ulster during the Confederate Wars of the 1640s. His children by her were 1. Aodh Ruadh, his only legitimate son, who was killed by the Cromwellians; 2. Eibhlin, who married Colla Dubh Mac Mahon, and whose son was Most Reverend Hugh MacMahon, Roman Catholic Archbishop of Armagh; 3. Maire, who married firstly Aodh Maguire and secondly Ruaidhri Og Maguire, the 5th Lord Enniskillen.