The MacNaughton family opposed Robert the Bruce in his attempt to gain the throne of Scotland and, as a result, forfeited many of their lands when he became king. The fortunes of the clan were somewhat restored by David II when he granted them lands in Lewis.
The direct line of the MacNaughtons died out around 1700 with John MacNaughton, who tried to salvage his fortunes by marrying the second daughter of Sir James Campbell of Ardkinglass. Sir James, however, tricked him into marrying his eldest daughter instead by plying him with drink until he was unable to fully comprehend what was happening. MacNaughton, when he sobered up, fled to Ireland with his original choice and Ardkinglass accused him of incest. MacNaughton was found guilty and Ardkinglass was compensated with the remains of the MacNaughton property.
After this incident, the chiefship remained dormant until the nineteenth century when it was discovered that the direct line of the family could be traced to another John MacNaughton, known as ‘Shane Dhu’, who had emigrated to Antrim in 1580. His great-grandson Alexander was recognised as chief of the clan in 1818.