In 1569, during the Marian civil war between the deposed Mary, Queen of Scots and James VI of Scotland, a feud arose between the Clan Mackenzie and Clan Munro, who were among the most powerful clans in Ross-shire. The trouble started when John Leslie, Bishop of Ross granted to his cousin Leslie, the Laird of Balquhair, the right and title to the castle at Chanonry together with the castle lands. Bishop Leslie had been secretary to Queen Mary and there was strong feeling against episcopacy in Scotland. He therefore felt it best to arrange for the church property of his bishopric to pass into his family's hands to preserve some of the important privileges that he enjoyed as bishop. Notwithstanding this grant, the Regent Moray (James Stewart, 1st Earl of Moray), acting in the name of the infant King James VI, gave the custody of the castle to Andrew Munro, 5th of Milntown.