In 1591 he was appointed to the post of Lord High Admiral of Scotland following the disgrace of Francis Stewart, 5th Earl of Bothwell. On 18 October he was playing golf on the sands of Leith with the Earl of Huntly and they attempted to arrest Bothwell, who escaped, but Bothwell's horse "Valentine" was captured with Robert Scott brother of the Laird of Balwearie. Lennox arrested Michael Balfour of Burleigh and John Wemyss of Logie on 8 August 1592 on suspicion of conspiracy with Bothwell. They were interrogated at Dalkeith Palace. Burleigh was released and Logie escaped with the help of his Danish girlfriend Margaret Winstar.