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A brother-in-law of Oliver Cromwell, Jones was born at Llanbedr in North Wales and is often surnamed Jones Maesygarnedd after the location of his Merionethshire estate. Jones spoke Welsh with his family. He was an avid Republican at a time when most of Wales was Royalist, and for this reason he was described by one of his contemporaries as "the most hated man in North Wales".
During the civil war Jones served in the parliamentary forces in Wales, and was described as a colonel in 1646, while negotiating the surrender of Anglesey in June 1646. In 1648 he helped to suppress Sir John Owen's rising, was thanked by the House of Commons for his share in the reconquest of Anglesey, and was voted £2,000 on account of his arrears of pay. He was returned to the Long Parliament in about 1647 for Merionethshire.
Jones was selected as one of the judges of King Charles I, and attended the trial with great regularity up to the day he signed the King's death-warrant. After execution of the King, Jones was elected a member of the first two Councils of State of the Commonwealth
In July 1650 Jones was voted one of the commissioners to assist the lord deputy in the government of Ireland, and was reappointed for two years longer on 24 August 1652. His colleague Edmund Ludlow describes him as "discharging his trust with great diligence, ability, and integrity, in providing for the happiness of that country, and bringing to justice those who had been concerned in the murders of English Protestants".
Jones was a strong republican and was greatly dissatisfied at Cromwell's assumption of the Protectorate. Henry Cromwell describes him as "endeavouring to render the government unacceptable", but "more cunning and close" in his opposition than Ludlow. He was accordingly set aside, and when in March 1656, there was a rumour that Jones was to be again employed in the Irish government, Henry Cromwell remonstrated with Thurloe against the choice, asserting that he was not only factious and disaffected, but "had acted very corruptly in his place". But by this time a marriage had been arranged between Jones and the Protector's sister Catherine, widow of Roger Whitslone. "When I writ to you about Colonel Jones", explained Henry Cromwell. "I did not know that he was likely to be my uncle. Perhaps that may serve to oblige him to faithfulness to his highness and government".
In the First Protectorate Parliament (1656) he was returned for the counties of Merioneth and Denbighshire and chose to sit for Merioneth. In the Second Narrative of the late Parliament Jones is described as originally "one of good principles for common justice and freedom ... lately married the Protector's sister, by which means he might have become a great man indeed, did not something stick which he cannot well get down. He is not thorough-paced for the court proceedings, nor is his conscience fully hardened against the good old cause".
Jones was summoned to the Protector's Other House (December 1657), but held no office except that of governor of the Isle of Anglesey. On 2 June 1657 Parliament voted Jones Irish lands to the value of £3,000, for arrears of pay amounting to that sum. But he was still so far trusted by the republican party that on 7 May 1659 he was appointed one of the Committee of Safety, and on 14 May one of the Council of State.
An act was passed making Jones and others commissioners for the government of Ireland, 7 July. Jones landed in Ireland with Ludlow in July 1659, and when the latter returned to England in October following, he selected Jones to command the Irish forces during his absence. To Ludlow's disgust Jones and most of the Irish officers supported John Lambert and the army in their quarrel with the parliament. When Ludlow expostulated Jones made the excuse that he acted at the "incessant importunity of others", and begged Ludlow to return and ease him of the burden of his command  On 13 December 1659, however, Colonels John Bridges, Theophilus Jones, and other officers of George Monck's party seized Dublin Castle and arrested Jones. An impeachment of high treason against Jones and his colleagues (Ludlow, Corbet, and Thomlinson) was presented to Parliament on 19 January 1660. The main charge was that he had "openly and publicly owned that treacherous and traitorous act of part of the army in England in their unjust force put upon the parliament". Jones was summoned before the council of state, but released on an engagement not to disturb the existing government.
As a political active senior member of the republican party, who had married into Protectors' family and an opponent of Monck's party, the Restoration of the monarchy under Charles II exposed Jones to certain ruin, but he seems to have been unaware of the danger he was in, and made no attempt to flee. He was arrested on 2 June 1660, as he was quietly walking in Finsbury, and was committed to the Tower of London. On 4 June the House of Commons excepted him from the Act of Indemnity, and he was tried on 12 October the same year. Jones confessed that he had sat among the king's judges, made no attempt to plead any point of law, and was sentenced to death. He was executed, together with Adrian Scroop, on 17 October 1660, and died with great courage and dignity.
Jones married twice. His first marriage was before 1639 to Margaret Edwards (died Ireland 19 November 1651) they had eight children but only one, a son, survived him. Margaret was a devoted follower of the Puritan preacher Morgan Llwyd.
In 1656 Jones married again. His second wife was Catherine Whitstone (baptised on 7 February 1597), the third sister of Oliver Cromwell, and the widow of Roger Whitstone a Parliamentary army office who had campaigned in the Low Countries, she had three sons and two daughters. She received an annual settlement of £300 from the estate of her former husband to which Oliver Cromwell added an annuity of £150. She and Jones had no children. Her husband opposed Richard Cromwell when he was Protector, and Richard stopped her annuity. From a letter of hers that was published in the 19th century it seems that she had Royalist sympathies as she disproved of the execution of Charles I.
After Jones's execution his son and heir was allowed to retain the lands Jones had held before 1646, but the rest either returned to the Crown (if they had been Crown lands before the Civil War) or were forfeited. His forfeited estates in Wales went to the Duke of York (the future James II of England, while those in Ireland went to Arthur Annesley, 1st Earl of Anglesey.
- Dodd 2009.
- Roberts 2004.
- Firth 1892, p. 125 cites Williams Eminent Welshmen, 1852. p. 257.
- Firth 1892, p. 125 cites Pennant, Journey to Snowdon, ed. Rhys. ii. 265.
- Firth 1892, p. 125 cites 4 October 1648; Commons' Journals, vi. 43.
- Firth 1892, p. 125.
- Firth 1892, p. 125 cites Noble, Lives of the Regicides, i. 372.
- Firth 1892, p. 125 cites (Return of the Names of the Members of Parliament, i. 499); Godwin Commomwealth of England, iii. 15, 178.
- Firth 1892, p. 125 cites Commons' Journals, vi. 434, vii. 167.
- Firth 1892, p. 125 cites Edmund Ludlow Memoirs, ed. 1751, p. 370.
- Firth 1892, p. 125 cites Birch 1742, p. 149.
- Firth 1892, p. 125 cites Birch 1742b, p. http://india.british-history.ac.uk/image-pageScan.aspx?pubid=612&sp=1&pg=606 606.
- Firth 1892, p. 125 cites Birch 1742b, p. 672
- Firth 1892, p. 126 cites Harleian Miscellany, ed. Park, iii. 485.
- Firth 1892, p. 126 cites Commons' Journals, vii. 492, 543.
- Firth 1892, p. 126 cites Commons' Journals, vii. 646, 654.
- Firth 1892, p. 126 cites Commons' Journals, vii. 707; Ludlow Memoirs, p. 268.
- Firth 1892, p. 126 cites Ludlow Memoirs, pp. 279, 282.
- Firth 1892, p. 126 cites Ludlow Memoirs, p. 299.
- Firth 1892, p. 126 cites Commons' Journals, vii. 815.
- Firth 1892, p. 126.
- Firth 1892, p. 126 cites Ludlow Memoirs, p. 331.
- Firth 1892, p. 126 cites Ludlow Memoirs, p. 346; Mercurius Publicus, 31 May–7 June 1660.
- Firth 1892, p. 126 cites Trial of the Regicides, 1660, pp. 95–100.
- A full account of his behaviour and last utterances, with a sketch of his life, is given in A Complete Collection of the Lives, Speeches, Private Passages, Letters, and Prayers of those Persons lately executed, with Observations by a Person of Quality, 8vo, 1661, pp. 135–46. (Firth 1892, p. 126)
- "Notes and Queries,' 7th ser. ix. 303." (Firth 1892, p. 126).
- Birch, Thomas, ed. (1742). 'State Papers, 1654: March (2 of 5)', A collection of the State Papers of John Thurloe 2. pp. 140–151.
- Birch, Thomas, ed. (1742b). 'State Papers, 1656: March (4 of 8)', A collection of the State Papers of John Thurloe, volume 4: September 1655 - May 1656 4. pp. 604–615.
- Dodd, Arthur Herbert (2009). "JONES , JOHN, Maes-y-garnedd, Merioneth". Welsh Biography Online. The National Library of Wales. Retrieved July 2012.
- Roberts, Stephen K. (2004). "Jones, John (c.1597–1660)". Oxford Dictionary of National Biography. Oxford University Press. doi:10.1093/ref:odnb/15026.
- This article incorporates text from a publication now in the public domain: Firth, Charles H. (1892). "Jones, John (d.1660)". In Lee, Sidney. Dictionary of National Biography 30. London: Smith, Elder & Co. pp. 125,126. Endnotes:
- Ludlow's Memoirs, ed. 1751, fol.
- Noble's House of Cromwell, ed. 1787, ii. 213;
- Phillips's Civil War in Wales, 1874
- Official letters from Jones during his employment in Ireland are printed in the Thurloe Papers, in Cary's Memorials of the Civil War, and in the Proceedings of the Liverpool Historic Society for 1860–1, pp. 177–300.