The original fortification at Markree was a 14th-century McDonagh outpost guarding the ford across the Unshin. In 1663, after Cromwell's army defeated the O'Brien Clan in the wars of the 1640s and 1650s, the lands were granted to Cornet Edward Cooper, who had served under Cromwell himself. The defeated clan chief, Conor O'Brien, had died in the fighting. Cooper married his widow - Marie Rua, "Red Mary," already a famously formidable figure in Irish history - and her sons were divided between estates. One inherited Dromoland in County Clare; the other got Markree. Charles Cooper, the last of the Cooper line at Markree, was a direct descendant. The marriage that secured the holding outlasted the war that won it.

In 1830, Colonel Edward Joshua Cooper - eldest son of the MP, grandson of the Governor of Bengal on his mother's side - founded an observatory in the castle grounds. He had money, education, and the kind of patient obsession that finds new worlds. His refracting telescope, mounted under a dome at Markree, was for a stretch of years the largest such instrument on Earth. The Royal Astronomical Society in 1851 called it "undoubtedly the most richly furnished private observatory known." Cooper and his assistant Andrew Graham used it to discover the asteroid now catalogued as 9 Metis in 1848 - a real cosmic body found from a small dome in County Sligo. The observatory ran until Edward Henry Cooper died in 1902.

On 16 January 1881, the thermometer at Markree Castle recorded the lowest air temperature ever officially logged in Ireland. The number itself - minus 19.1°C, by Met Éireann's reckoning - is striking enough, but more striking is the image of it: a winter night so still and clear that the limestone-vaulted air above the Unshin froze to a record nobody has yet beaten. The castle, by then in the second generation of its Victorian astronomical fame, was an ideal place to be making measurements. There was already a tradition of careful instruments in careful hands. A separate tradition holds that Cecil Frances Alexander wrote her hymn "All Things Bright and Beautiful" while a guest at Markree in 1848. If true, she watched a different kind of sky from these same windows.

Bryan Cooper, soldier and politician, inherited in 1902 and lived in the castle until his death in 1930. The Coopers continued, though by the 1980s the castle was largely empty, briefly waking only for a 1988 television miniseries based on J.G. Farrell's novel Troubles. Charles Cooper, the tenth generation of his family to live at Markree, opened it as a hotel in 1992 - rescuing it the way most great houses in Ireland have had to be rescued, by inviting strangers to sleep in the bedrooms. In 2015, after almost four hundred years, the Coopers finally let go. The Corscadden family, who run a small group of Irish castle hotels, took over and refurbished the place. The 300-acre estate still holds red squirrels, otters, and kingfishers along the Unshin's banks. Inside, the Louis Philippe plasterwork in the dining room and the stained glass window of Coopers stretching back to King John are still doing the work they were built to do: telling guests where they are.