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 his commission was terminated, by the king's resolution to make the young Duke of York lord high admiral. He was a very regular attendant at the meetings of the council held every Sunday, and meetings of the admiralty board were constantly held at his own house. He thus exerted a general supervision over all departments of the government. On 10 April 1636 he was put on the commission for the government of all colonies planted by English subjects. From the time of the first exaction of ship-money he was constantly engaged in receiving reports respecting its collection. His heavy work was rendered more difficult by disputes among his colleagues. Windebank and Laud had quarrelled, and Juxon tried in vain to be the peacemaker. In August 1636 he was present at Laud's reception of the king and queen at St. John's College, when the new library and rooms were thrown open. Juxon had directed the early stages of the building on behalf of the donor, and had hit upon the marble used for the pillars while engaged in his favourite sport of hunting.

The reckless extravagance of the court was an incessant source of trouble, and his anxieties were increased tenfold by the outbreak of the Scots war. On 10 Jan. 1638–9 he was added to the committee of the council of war, and he served on all the smaller committees for administrative purposes into which the council was divided during the king's absence in the north. While the Short parliament was sitting Juxon was busily writing letters on the king's order for the levying of a forced loan within ten days (to Sir R. Wynn, 10 April 1640, Fairfax Correspondence, ed. Johnson, i. 402). Juxon was summoned as a witness at the trial of Strafford, but, like Hamilton, Northumberland, and Cottington, could remember nothing of the suggested employment of the Irish army in England, which Vane attributed to Strafford. When the attainder was passed by the lords, Juxon and Usher alone advised Charles to refuse his assent, ‘seeing he knew his lordship to be innocent.’ He visited Laud in the Tower, and on 17 May 1641 he resigned the treasurer's white staff. While other bishops were impeached and imprisoned, he was left to reside peaceably at Fulham. ‘Neither as bishop or treasurer,’ says Sir Philip Warwick, who had been his secretary, ‘came there any one accusation against him in that last parliament, whose ears were opened, nay, itching, after such complaints;’ and Falkland, in an attack on the episcopate, made an honourable exception in his favour, ‘that in an unexpected place and power he expressed an equal moderation and humility, being neither ambitious before, nor proud after, either the crozier or the white staff.’ On 17 Aug. 1641 he had to pay part of a fine levied by the House of Lords on the judges of the high commission for exceeding their powers in the case of one Ekins. In 1643 he was obliged to pay 500l. to the support of the parliamentary army (Calendar of Committee for Advance of Money, pt. i. p. 229). He was not otherwise molested, and he seems for a while to have been crippled by illness (Nicholas to the king, 5 Oct. 1641, in, Diary, Appendix, ed. Wheatley). The letters of Sir Edward Nicholas show that the king, now that Laud was in the Tower, took Juxon's advice on the appointments to vacant bishoprics.

During the troubles of the next few years, ‘when the king was admitted to any treaty with the two Houses' Commissioners, he always commanded [Juxon's] attendance on him. …’ ‘This,’ the king said, ‘I will say of him, I never got his opinion freely in my life but when I had it I was ever the better for it’. In the autumn of 1646, when Charles had concocted a scheme for the discussion of religious differences which was to lead to an establishment of presbyterianism, he wrote privately (30 Sept. 1646) to Juxon asking whether he might ‘with a safe conscience give way to this proposed temporary compliance’ (, Original Letters, 2nd ser. iii. 325). Juxon (and Brian Duppa, bishop of Salisbury), in reply, 14 Oct. 1646, acknowledged the wisdom of such tolerance during a period of conference (Clarendon State Papers, ii. 267). Juxon was with the king at the date of the negotiations of Newport in 1648, and during his trial. After the sentence he rarely left him, and the king declined the company of other ministers. On the morning of 30 Jan., the day of the execution, the bishop, after private prayers, read the morning service with the king, and alone of his servants was with him on the scaffold. To him and Colonel Tomlinson the king handed a copy of his speech in vindication of his government, and, in answer to Juxon's request, added his profession of loyalty to the church. Charles also gave Juxon a copy of his private prayers, printed in some copies at the end of the ‘Eikōn basilikē’ (see the controversy between Wordsworth and Todd, and the latter's Letter to the Archbishop of Canterbury, 1825). Juxon took leave of his master in the words, ‘You are exchanged from a temporal to an eternal crown, a good exchange,’ and as Charles laid his head on the block, he gave the bishop his last commission in the word ‘Remember!’ The paper handed by the king to Juxon, containing a note of his speech, was at once de-