There was civil strife among the Cenell Eoghain; Shane was victorious, Ferdoragh was killed, Conn was permanently driven out of Tyrone, and died in the Irish Pale in 1559, the area of Ireland directly governed by the English.

In English law, Ferdoragh's eldest son, Brian O'Neill, then succeeded to the Earldom; in practice he continued to be called Lord Dungannon.

Queen Elizabeth I, newly come to the throne, proposed to recognize Shane as Earl, since he actually ruled Tyrone and was the eldest legitimate son; but the negotiations collapsed.

[2] Brian was killed in 1562, while still young and unmarried, by his cousin Turlough O'Neill, the tanist of his uncle Shane (and a grandson of the brother of Conn Bacagh, the first Earl).

Despite the Anglo-Spanish peace treaty of 1604, in 1607 O'Neill, his brother-in-law the Earl of Tyrconnell, and several of their followers fled to Europe, expecting the Spanish to invade Ireland with an army.

The Barony of Dungannon created for Matthew or Ferdoragh O'Neill was limited, by the terms of the patent, to his descendants who were heirs apparent to the Earldom of Tyrone.

"Though no longer recognized in England, it was granted by Spanish kings to a line of O'Neills in rightful succession to the end of the seventeenth century".

Not all the claimants to the Gaelic offices claimed the Earldom: the descendants of Shane the Proud were inaugurated as the O'Neill by the ancient ritual, by which the O'Hagan put golden shoes on their feet on May Eve, without calling themselves Earls.

Don Jorge O'Neill of Clanaboy and Lisbon submitted his pedigree to the Ulster office of Heralds; in 1895 the genealogy and arms were confirmed.

Although collateral descent from the grantee does not confer a peerage, he assumed the style of Conde de Tyrone, but his descendants use the title Prince of Clandeboye.

Queen Victoria's recognition was followed by those of the Pope, the kings of Spain and Portugal, and the Republic of Ireland in 1945 as the Prince of Clandeboye.