With his second wife Elizabeth, daughter of Sir Thomas Herbert, 1st Baronet, who was living on 25 May 1686 (the date of her last letter to Muggleton), Phayre had three sons and three daughters.
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He was one of the three officers to whom the warrant for the execution of Charles I was addressed, but he escaped severe punishment at the Restoration through having married the daughter of Sir Thomas Herbert (1606-1682).
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With Francis Hacker and Robert Phayre, he was one of the senior army officers delegated to supervise and carry out the King's execution.