The Reformation brought a new bitterness to the struggle between Gaelic and Catholic Ireland and their English rulers. It was an age of war, rebellions and plantation, of the Spanish Armada and Granuaile – Ireland’s Pirate Queen.

The Gaelic resurgence peaked in the late 15th and early 16th century when the now partially Gaelicized Fitzgeralds acted as the Crown’s Chief representatives in Ireland. Following an unsuccessful rebellion by Silken Thomas, the Earl of Kildare, in the 1530s, the Tudor dynasty began to re-establish English authority in Ireland. The situation was further complicated by the politics of the Reformation which gradually led to the alienation from the Crown of the old English settlers in Ireland who had largely remained Catholic. A series of military campaigns in the 16th century ultimately resulted in the collapse of Gaelic military power and the establishment of plantations of Protestant settlers in strategic areas. Following the battle of Kinsale and the defeat of Hugh O’Neill large scale colonisation took place in Ulster. This plantation ultimately led to further rebellion and the final conquest of Ireland during the Cromwellian period. The Gaelic lords, defeated and broken by the wars of the 1650s, were evicted from their lands and fled to France in huge numbers, to be replaced by an influx of new landowners, in what became known as Cromwell’s policy of “To Hell or to Connacht”. Subsequently, the Catholic Irish (who now included many of the Old English) placed their hopes in the House of Stuart who were suspected (correctly) to have Catholic sympathies. These hopes ultimately proved vain however and following the Glorious Revolution of 1688 and the subsequent war between James II and William III, which was largely fought in Ireland, the bulk of the land of Ireland ended in the hands of a newly established Protestant elite made up of a combination of English, Welsh and Scottish adventurers and anglicised elements of the old Gaelic and Old English aristocracy. Catholicism remained illegal in theory although widely practiced with official connivance (interspersed with regular periods of local persecution).

The military campaigns and unrest of the 15th, 16th and 17th centuries have left their mark on the landscape in the shape of monastic and church buildings unroofed and abandoned after the dissolution of the monasteries and a variety of military architecture. At a local level, rituals such as visiting holy wells and known pilgrimage destinations took on an increased importance among the Catholic population who remained largely alienated from the established church and many aspects and traditions surrounded popular pilgrimage destinations may date to this period. Towerhouses, the fortified dwellings of the Gaelic aristocracy, control many strategic anchorages along the west coast while English fortifications were established as far west as Aran and Inishbofin; the last strongholds to fall during the Cromwellian Wars. Arkin’s Castle in Killeany is an Eizabthan fort built on the likely site of an earlier O’Brien castle while Don Bosco’s Castle on Inishbofin is a star-shaped fort built by the Cromwellian garrison of the island in the 1650s. Star shaped forts were also built on Coney island in Sligo Bay and on Valentia Island. The establishment of a new elite, in many cases with no historic link to their extremely large estates, led to the wholesale clearance of early monuments in some places. One such outbreak of clearance work led to the discovery of the entrance to the Newgrange passage tomb by workers destroying a large cairn for the new landowner Charles Campbell.

Culturally, this period saw the Gaelic learned classes go into decline as their patrons lost power and influence or fled to the continent. Elements of the Gaelic poetic and historical tradition survived however into the 19th century with poets such as Mac Suibhne and Raftery attempting to continue their traditional lifestyle and individual manuscripts and relics remaining in the hands of specific local families. The 17th century saw the last major works of the native Irish historical tradition with the completion of Foras Feasa ar Éirinn by Geoffrey Keating, the compilation of the Annals of the Four Masters and Leabhar Mor Na nGenealach (the Great Book of Genealogies) by Dubhaltach mac Fhiribisigh. This late 17th century also coincided with the beginnings of Antiquarian scholarship in Ireland, spurred on by the visit of Edward Lhuyd in 1699, with Lhuyd’s correspondent Roderick O’Flaherty acting as a linking figure between the two learned traditions. Llhuyd’s work led to the first modern descriptions of many important monuments and spurred on the work of later Antiquaries such as Molyneaux, Vallancey, Pownall and Charlemont.