With some sympathisers among some of the Highland clan chiefs - who, by definition, had their own private armies - the Jacobites attempted to restore the Catholic monarchy with various uprisings in which the Highlands played a part. Principal among these were the 1719 rebellion, when Eilean Donan Castle was destroyed by gunfire by British naval ships. Other fortified places were also affected by Jacobite activity - for example, Urquhart Castle was blown up in 1692 to prevent it falling into Jacobite hands. However, the Jacobite clans were finally defeat by the government army at Culloden Moor, near Inverness. This made their leader, Prince Charles Edward Stuart, aka Bonnie Prince Charlie, a Highland fugitive, most famously in Knoydart and Skye.

Charles was in Scotland less than a year and only raised about 6000 of the 30000 fighting clansmen in the Highlands. Yet within a few generations, his hopeless escapade had been transformed into a romantic cause, while Charles became one of the most dashing figures in the story of the Highlands. However the reality was that the aftermath of Culloden was to ultimately end the old-style clan life. Emigration, the Clearances, sheep and sporting estates followed on over the next century.