Donald, son of Farquhar, married Isobel Stewart, the heiress of Invercauld. Their son, Findlay Mor, became the first Farquharson of Invercauld. He fell at the Battle of Pinkie (1547) where he was the Royal Standard bearer.

    There developed many other branches of Farquharsons, notably the Farquharsons of Monaltrie and Inverey who followed Montrose and fought under Charles II at Worcester in 1651 where Charles was defeated.

Later that century, "Bonnie Dundee" had the Farquharsons' support for his forces -- including John, third Laird of Inverey, known as the Black Colonel. He is remembered in ballad and legend, and for his daring escape from the Hanoverians when he rode his horse up the dangerously sheer, craggy side of the Pass of Ballater.

Rising of 1745
During the rising of 1745, the chief of MacKintosh was Angus, who was an officer in the Black Watch, fighting against the Jacobites. His wife, however, was Anne, daughter of Farquharson of Invercauld, and she rallied the Clan MacKintosh to fight under Clan Chattan for the Jacobite cause. When Angus was captured at the Battle of Prestonpans, he was sent home to his wife. Anne greeted him with the words, "Your servant, Captain". He famously retorted, "Your servant, Colonel". From then on she has en known as Colonel Anne. After later saving Bonnie Prince Charlie from capture at one point, Colonel Anne was imprisoned at Inverness for six weeks. At Cullodon, in 1746, some three hundred clansmen led by Farquharson of Monaltrie were in the front lines on that fateful day.