Tomaidh Mohr (or Big Thomas in English), who gave this clan its name, was descended from a grandson of William MacKintosh, 8th Chief of Clan Chattan. Tomaidh and his kinsmen formed a new settlement at Glen Shee, in Perthshire. The clan centre was Thom, on the East Bank of Sheerwater, but this changed in 1600, when Robert MacComie, the 4th Chief, was murdered. His brother, John MacComie, the 7th Chief, resented tax collectors. He once hired an Italian assassin to deal with them, but the next taxman proved the better swordsman, and killed the Italian.
The clan played a prominent role in the Civil War. Initially, John MacComie, 7th Chief, supported the Royalists, fighting alongside the MacKintoshes in 1644. Later, he switched allegiance, and the family suffered badly after the Restoration. By the end of the century, the clan was drifting apart, with some members moving to Angus and Fife. Here they were known as Thom, Thomas, or Thompson.