The fortress was taken from O’Donnell’s warders in 1496 by his son Hugh. His brother Con, with the assistance of Maguire, laid siege to the castle and dislodged him. O’Neill possessed himself of the stronghold in 1522, and slew the warders. It seems to have remained in his possession until Sir Henry Sidney came north in 1566 and had it delivered to him, as well as the castles of Donegal, Beleek, Bundrowes, and Castle Sligo. All these fortresses he placed in the hands of O’Donnell and his allies, who were at this time in high favour with England. The next year Shane O’Neill liberated Con O’Donnell and his brother, who were at the time his prisoners, and the castles of Ballyshannon and Beleek were delivered to Con. About this time the Government began to look with alarm on the growing power and popularity of the O’Donnells, and the State Papers of the period contain notes regarding the advisability of garrisoning Ballyshannon and the other fortresses of Tirconnell. The regular military force under O’Donnell consisted of 1,500 foot and 300 horse, out of which the garrison of Ballyshannon numbered 200 foot soldiers and 40 mounted men. In 1584, Lord Deputy Perrot recommended the erection of a castle and bridge at Ballyshannon, no doubt to counteract the power of the O’Donnells’ fortress, which could hold the main ford against all comers. Four years later the Lord Deputy dates a letter from Ballyshannon, and about this time young Hugh O’Donnell was kidnapped and imprisoned in Dublin Castle. In 1592, Mr. Ralph Lane applied to Burghley, asking for the custodianship and fee-farm of the castle and lands of Ballyshannon, &c. The successful escape of Red Hugh, however, from Dublin Castle seems to have placed the possibility of the Government’s disposing of his ancestral home quite out of the question, and in 1592 the greatest of the O’Donnells received a most royal welcome from his father’s dependents in the north. Arriving at Ballyshannon, where the O’Donnell warders still guarded the fortress, the whole country flocked to meet him and offer their congratulations on his escape. The neighbourhood was in the most fearful state, being entirely overrun by freebooters, against whom even the English were powerless--the castles of Ballyshannon and Donegal alone remaining in the hands of the O’Donnells. After a most successful campaign against the marauders, Hugh O’Donnell returned to Ballyshannon to undergo medical treatment for his feet, which had been fearfully injured by travelling from Dublin to Glenmalure in his house-shoes over the mountains and in bitter cold. He did not recover entirely until the end of the year, as both his great toes had to be amputated.