In 1643 Hugh Mackay, 2nd of Scoury was appointed as a commissioner of supply for the shire of Sutherland. In 1648 he was made a member of the War Committee but in 1649 was taken prisoner at Balvenie Castle during the Civil War. In 1650 Parliament appointed him as a colonel in a fencible regiment and he was re-appointed as a commissioner of supply in 1661. For his support of Charles II of England during the Civil War his estate was burdened with fines and debts, however his son, General Hugh Mackay, managed to clear them away. Hugh Mackay, 2nd of Scoury married Ann, daughter of John Corbett of Arkboll, Ross and had the following children: