The traditional history and genealogy of the Clan traces it's origins to one Gilliecatton Mor, a grandson Muirich (or Murdoch), a became the Parson of Kingussie. From him came a family name of Mac-a-Phersain, the son of the parson which developed into MacPherson later on. At the same time, it was held that the original name of the MacPhersons was Cattanach. Whatever the real facts, it appears to be fairly evident that the MacPherson family was, if not the most ancient family of Clan Chattan, then one of the earliest.

The Clan MacPherson territory of Upper Speyside came to this family at the time of Robert the Bruce, for whom they had fought at Bannockburn, tin return for helping to drive the Comyns from all of Badenoch. The task was undertaken and completed, and the Sons of the Parson moved in forthwith, becoming neighbours of the Mackintoches of Moy. In time, a MacPherson girl, Eva, married into the Moy family, and this union was the instance upon which the Mackintosh claim for the chieftainship of Clan Chattan was based.

Ewen MacPherson of Cluny joined the Stewart army with about six hundred men immediately after the Battle of Prestonpans. At Falkirk they formed the front line and were acknowledged as the finest of all troops in the entire command. But they missed Culloden, for they had been sent to guard the passes in the Badenoch. In the meantime, Cluny's house was burnt to the ground and all his possessions looted, so he had, after the defeat of Drumossie Muir, to scatter his men and seek refuge. His wife, too, having been driven from her home, had to find shelter and aid and did succeed in taking temporary refuge in a disused kiln elsewhere in the district.

Meanwhile, Cluny crept down Loch Ericht with a small party of men and accommodated himself in the cave which since has become known as Cluny's cage on the side of Craig Dhubh. Here, he was joined by Prince Charlie, who remained there in hiding until mid-September of 1746, from whence he left for Skye and eventually France.

Cluny remained in the concealment for nine years. Many people knew of his whereabouts, but despite enormous rewards of as much as a thousand pounds being offered for information leading to his apprehension, no tongue betrayed him. In 1765 he escaped to France and died soon afterwards.