The MacKinnons traditionally held lands in Mull and Skye, including the castle of Dunakin, a broch commanding the narrow sound between Skye and the mainland. Even in the early days they were an enterprising family, and from Dunakin they ran a heavy chain across the sound and levied a charge on all passing ships.

The MacKinnon clan maintained regular feuds with their neighbours, the MacLeans, though not always resorting to bloodshed to win the upper hand in these encounters.

During the civil wars the Mackinnons joined the standard of the Marquis of Montrose, and formed part of his forces at the battle of Inverlochy, Feb 2, 1645. In 1650, Lauchlan Mackinnon, the chief, raised a regiment of his clan for the service of Charles II, and, at the battle of Worcester, in 1646, he was made a knight banneret. His son, Daniel Mohr, had two sons, John, whose great-grandson died in India, unmarried, in 1808, and Daniel, who emigrated to Antigua, and died in 1720. The latter's eldest son and heir, William Mackinnon of Antigua, an eminent member of the legislature of that island, died at Bath, in 1767.

The Mackinnons engaged in both rebellions in favour of the Stuarts. In 1715, 150 of them fought with the Macdonalds of Sleat at the battle of Sheriffmuir, for which the chief was forfeited, but received a pardon, 4th January 1727. In 1745, Mackinnon, though then old and infirm, joined Prince Charles with a battalion of his clan. President Forbes estimated their effective force at that period at 200 men. After the battle of Culloden, the price, in his wanderings, took refuge in the country of the Mackinnons, when travelling in disguise through Skye, and was concealed by the chief in a cave, to which Lady Mackinnon brought him a refreshment of cold meat and wine.

The clan MacKinnon was long known for its loyalty to the Stewart monarchy and were 'out' in the Jacobite risings of 1715 and 1745. After the defeat at Culloden, Iain Og, the chief of the MacKinnons sheltered Charles Edward Stewart and aided him in his escape, although he was over seventy years old at the time. He was captured on returning from this adventure and held on a prison ship for four years.