Cowper, John a Scotch clergyman, brother of the bishop of Galloway, was a supply at the High Kirk, Edinburgh, in 1586, and became afterwards minister. He refused to pray for queen Mary in the terms of the king's command, for which he was imprisoned in the castle of Blackness; the city paid his expenses, obtained his release, and he was transferred to the Collegiate Church, Glasgow, in 1587, having charge of the eastern district and parish. He was a member of the assemblies of 1593 and 1596, and. was appointed to visit that at Lothian in 1602. In 1595 his life was threatened by two men, but the chief offender begged pardon on his knees before the presbytery. He died December 25, 1603. See Fasti Eccles. Scoticanae, 1:7; 2:7.