The priory was founded in 1225 by William Marshall the younger, Earl of Pembroke, who died in 1231.
In 1349, the community within the priory was severely affected by the outbreak of bubonic plague known as the Black Death. Eight members of the community died in three months during this pandemic. After the plague years, very few structural changes were carried out at the priory up until the end of 15th century. In 1540, Ireland was under the rule of Elizabeth I of England, a Protestant queen, and the property of the priory was confiscated by the crown. Elizabeth died in 1603, but the new King, James I, was no kinder to the priory: it became a courthouse, and the Dominicans were forced to leave and find places to stay in other houses.
From 1642 to 1649, Black Abbey played a major part in attempting to save both the Irish religion and the king, Charles I of England and of Ireland; the abbey hosted the government known as the Irish Catholic Confederation. These glory hours did not last long however. In March 1650, the English army under the command of Oliver Cromwell surrounded Kilkenny in a siege. Many people died from epidemic and hunger, many more fled before the city finally surrendered.
From 1685 to 1689 under the rule of the Catholic king James II of England, the abbey flourished, but in 1690, under the rule of the Protestant king William III of England, both Kilkenny and the abbey were once again occupied by the English.
By 1776, the community of the Black Abbey was close to zero, but starting in that year, the Dominicans retook possession of the abbey, first by renting it. In 1816, Black Abbey was restored as a Dominican priory, and the first public mass was held on September 25th, 1816.
On Trinity Sunday, 22nd of May 1864, Black Abbey was reconsecrated by the bishop, and was finally opened again as a house of prayer.
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