[2] Clarke married Margaret Bourne of Bury St Edmunds, Suffolk, and had a son Samuel who was created baronet in 1698, and a daughter.
[2] In August 1654, he was returned to the First Protectorate Parliament as one of the two members for the three Irish counties of Donegal, Londonderry, and Tyrone and sat till January 1655.
[7] In April 1660 he was re-elected MP for Bury St Edmunds for the Convention Parliament when he was involved in a double return.
[2] In 1647, Clarke took up the accusation against the Eleven Members of the Peace Party in Parliament.
He was sent as Lieutenant Colonel Clerke with Admiral Blake to reduce the Scilly Isles in May 1651.
[8] Clarke was granted a Foot regiment on 16 June 1659 by the Committee of Safety, but was cashiered with Lambert and the other generals by the Council of State.
[1] Clarke was a prisoner in the Gatehouse on 17 December 1660, when he petitioned the King for his release, stating that he "was imprisoned on suspicion of treason, of which he knew nothing, nor had he in the least misdemeaned himself.