The Muscraige, from whom Muskerry takes its name, claimed descent from Corc, a son of Cairbre Musc. Their petty kingdoms once scattered across the province of Munster, but the largest centred on the present baronies of Muskerry West and Muskerry East. The septs were pre-Eoganachta, meaning their lineage predates the dominant Munster dynasty of the 6th century onwards. A pedigree of the Muscraige chieftains survives in the Book of Leinster. At the time the territory took its first known shape, it did not extend south of the River Lee, even though the river now bisects the barony. The original Muscraige did not need to cross the water; the south bank was somebody else's country.

Around 1096, the kingdom of Muscraighe Mittaine fell to the O'Flynns, who had been displaced from Eoganacht Locha Lein by the rising O'Donoghues. The local O Donnagain dynasty kept up opposition long enough to kill the reigning O'Flynn king of Muskerry in 1115, after which both families slid into obscurity. From 1118 onwards the kings of Desmond came from the leading family of Eoganacht Chaisil, the MacCarthy dynasty. In 1171, the reigning king Dermod Mor MacCarthy submitted to Henry II of England, hoping to secure the king's protection against the king's own land-hungry barons, in the Gaelic style. Instead, Henry granted Dermod's entire kingdom to two adventurer knights, Robert Fitz-Stephen and Milo de Cogan, in 1177. The MacCarthys were left paying rent on their own land.

When King John came to the throne in 1199, he was determined to weaken the Irish barons. He sequestered the kingdom of Desmond and from 1200 to 1207 he parcelled it out among his loyal subjects. Richard de Cogan, nephew of Milo, got Muscraige Mittaine but was expected to win it by the sword. The de Cogans built castles at Mourne Abbey, Maglin near Ballincollig, Dundrinan, Dooniskey, Mahallagh, and Macroom. By 1242 John de Cogan held the patronage of three local churches. The de Cogans never fully consolidated power. Following the Battle of Callann around 1261, the MacCarthys successfully repulsed the Cambro-Normans, though their leader Finghin Mac Carthaigh was killed. In 1280 the MacCarthy Reagh sept of Carbery made peace with the main MacCarthy branch and they apportioned Desmond between themselves. The Cogans gradually lost their power and lands in Muskerry. By 1398 the MacCarthys were free to plunder from Dingle to the territory of the Barretts.

Twelve civil parishes lie partly or wholly inside Muskerry West. They include Macroom itself, plus Clondrohid, Inchigeelagh, Kilmichael, Kilmurry, Drishane, and others. The parish of Macroom is unusually complicated, with three exclaves mostly enclosed by Clondrohid and a third sitting between Clondrohid and Aghabulloge in Muskerry East. Twenty-four of the twenty-six townlands of Kilmurry lie in Muskerry West; the other two are in Muskerry East. Forty-six of fifty-two townlands of Drishane lie here; six are in Duhallow. 107 of 118 townlands of Inchigeelagh are in Muskerry West; eleven are in Carbery East. Two-thirds of Kilmichael is here. These are the kinds of boundary irregularities that survive from centuries of sept territory, monastic land grants, and chieftain trades. They make no sense on a modern administrative map. They make perfect sense if you know who fought whom in 1280.

What survives across Muskerry West is more than borders. The barony holds megalithic complexes at Carrigagulla, close to Ballinagree, and at Knocknakilla, between Millstreet and Clondrohid: standing stones, stone circles, ceremonial alignments from a thousand or two thousand years before the Muscraige claimed the land. The O'Learys, originally chiefs of country around Rosscarbery, moved here around the time of the Anglo-Norman invasion and became lords under the MacCarthys of the country between Macroom and Inchigeelagh. In 1642, sixteen leading men of that name were attainted, legally stripped of civil rights, including Connor O'Leary of Carrignacurra and Auliff O'Leary of Cunnowley. The Irish speakers counted in 1871 were the great-great-grandchildren of those who saw the attainder. The language thinned over the following century but never entirely left. The barony is administratively obsolete. The land is not.