Popular tradition gives the clan a Dalriadic Gaelic origin. The 19th-century historianW. F. Skene named the clan as one of the seven clans of Siol Alpin, who according to Skene could all trace their ancestry back to Alpin, father of Cináed mac Ailpín. Popular tradition has been until recently to consider Cináed mac Ailpín the first King of Scots and a Gael, however recent research speculates Cináed was a Pictish king and possibly even a Pict himself. Sir Iain Moncreiffe of that Ilk speculated that Clan Mackinnon belonged to the kindred of Saint Columba, noting the Mackinnon Arms bore the hand of the saint holding the Cross, and the several Mackinnon abbots of Iona.
The Mackinnon clan took part in the thirty years war with neighbouring clans such as MacKay, Love and McFarlane. Early history states that the Mackinnon clan was one of the most powerful clans in highland Scotland.