During the Desmond Rebellion, the Fitzgeralds fought against the forces of Queen Elizabeth I in the region.
The Fitzgeralds, together with the other southern lords of the Hiberno-Norman stock (who had become "more Irish and the Irish themselves"), formed the Geraldine League to oppose the Queen's plan to force Protestantism on the Irish people and her attempt to rout the native chiefs and replace them with English landlords.
In 1581 the Earl of Ormond overran Imokilly; at Castlemartyr he captured the aged mother of the seneschal, John FitzEdmund, and hung her from the wall of the castle.
FitzEdmund eventually submitted to the Earl, but he did not recover his lands.
Instead, the property shared the fate of other properties after the Desmond Rebellion.
It was confiscated and included in the grant of land between Lismore and Castlemartyr that were given to Sir Walter Raleigh.
FitzEdmund himself was arrested in 1585 and died in Dublin Castle in the following year.
In 1602, Raleigh's lands around Castlemartyr were bought by Richard Boyle, the First Earl of Cork and ancestor to the Earls of Shannon.

By the early 17th century the FitzGeralds were a spent force.
 In the south-east corner of the old church in Ballyoughtera, the stone has a boar crest surrounded by triple incised circles and shallow cross carving which is also encircle.
At the northern end of Ballyoughtera church ruin is the grave of another Richard Boyle, the 4th Earl of Shannon who died in 1868.
This tomb bears the inscription, "A sorrowing wife placed this stone in memory of the best and most affectionate of husbands".
During the Desmond Rebellion, the Fitzgeralds fought against the forces of Queen Elizabeth I in the region. The Fitzgeralds, together with the other southern lords of the Hiberno-Norman stock (who had become "more Irish and the Irish themselves"), formed the Geraldine League to oppose the Queen's plan to force Protestantism on the Irish people and her attempt to rout the native chiefs and replace them with English landlords. In 1581 the Earl of Ormond overran Imokilly; at Castlemartyr he captured the aged mother of the seneschal, John FitzEdmund, and hung her from the wall of the castle. FitzEdmund eventually submitted to the Earl, but he did not recover his lands. Instead, the property shared the fate of other properties after the Desmond Rebellion. It was confiscated and included in the grant of land between Lismore and Castlemartyr that were given to Sir Walter Raleigh. FitzEdmund himself was arrested in 1585 and died in Dublin Castle in the following year. In 1602, Raleigh's lands around Castlemartyr were bought by Richard Boyle, the First Earl of Cork and ancestor to the Earls of Shannon.
By the early 17th century the FitzGeralds were a spent force.  In the south-east corner of the old church in Ballyoughtera, the stone has a boar crest surrounded by triple incised circles and shallow cross carving which is also encircle. At the northern end of Ballyoughtera church ruin is the grave of another Richard Boyle, the 4th Earl of Shannon who died in 1868. This tomb bears the inscription, "A sorrowing wife placed this stone in memory of the best and most affectionate of husbands".
Castlemartyr