 He married, first, Ellen or Helen, daughter of Maurice Roche, 6th Viscount Fermoy, and Eleonor FitzGerald, who died in 1597; by her he had one daughter, married to Cormac, son and heir of Lord Muskerry.His second wife, who died on 12 January 1617, was Elizabeth, fourth daughter of Gerald FitzGerald, 11th Earl of Kildare and Mabel Brown; by her he had Henry O'Brien, 5th Earl of Thomond, and Barnabas O'Brien, 6th Earl of Thomond.Thomond's second brother, Teige, was long imprisoned in Limerick on account of his rebellion, but was released on protesting his loyalty; after another imprisonment he joined in O'Donnell's second invasion of Clare in 1599, and was killed during Thomond's pursuit of the rebels.