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H of Wight on the 25th, on the evening of which day, in acknowledgment of his gallant conduct, he, together with Frobisher (or Frobiser) and Lord Thomas Howard, was knighted by the lord admiral on the deck of the Ark. When on the next day the fleet was joined by the squadron of the Narrow Seas under Lord Henry Seymour [q. v.], Hawkyns, falling into the fourth place, became vice-admiral of Howard's division, and in the early part of the decisive action off Gravelines on the 29th would appear to have had the actual command of the centre during Howard's temporary absence [see ]; beyond all question the Victory fully shared in the glories of the day.

When the accounts for wages, provisions, and equipment had to be settled, Hawkyns obtained the assistance of his brother-in-law, Edward Fenton, who was appointed his deputy ‘to enable him to draw up his accounts’ (Cal. State Papers, Dom. 14 Dec. 1588). It is true enough that Hawkyns complained of the work as burdensome, and that Elizabeth and her ministers exercised a supervision which he thought offensive; but those who have condemned the queen's conduct in this matter have apparently not known that she had clear reasons for doubting Hawkyns's integrity. That the payments were made out of Hawkyns's own pocket is contrary to certain fact (ib. 16 Jan. 1589; Hist. MSS. Comm. 12th Rep. App. pt. i. p. 12, October 1588).

About this time Hawkyns, in conjunction with Drake, is commonly said to have instituted the fund long known as ‘The Chest at Chatham.’ As treasurer of the navy he would naturally be consulted in such a business, and Drake was the right hand of the lord admiral; but their share in the matter has been much exaggerated. Instituted the fund certainly was, and was continued as a distinct charity for the relief of maimed and wounded seamen, till the beginning of the present century; in 1814 its revenues were finally united with those of Greenwich Hospital. The chest, from which it derived its name, was moved to Greenwich in 1845, and is still preserved in the museum of the Royal Naval College. Early in 1590 Hawkyns was associated with Frobiser in the command of a squadron sent to the coast of Portugal ‘to do all possible mischief’ to the enemy, and especially to look out for the annual Plate fleet. This, however, having timely warning, did not appear; and the expedition returned to Plymouth without having accomplished anything, ‘and thus,’ wrote Hawkyns to Burghley on 31 Oct., ‘God's infallible word is performed in that the Holy Ghost said, “Pawle dothe plant, Apollo dothe watter, but God gyvethe the increase”’ (State Papers, Dom. Elizabeth, ccxxxiii. 118). It is said that the queen on reading the letter ejaculated, ‘God's death! This fool went out a soldier and has come home a divine.’

Hawkyns passed the years immediately following on shore. In November 1591 he was one of the commissioners ‘for taking account of the prizes taken at sea during the summer … and of the proper proportions to be assigned to her Majesty’ (Cal. State Papers, Dom.); proof sufficient that he had not forfeited the queen's confidence. On 8 July 1592 he wrote to Burghley that he had his leg hurt at the launch of the Swiftsure (ib.) He was at this time also engaged in the building and organising the still existing ‘Sir John Hawkyns's Hospital’ at Chatham, which was built in 1592, though the charter was not granted till two years later. Towards the end of 1594 he was again called on to serve at sea, in an expedition ordered to the West Indies, under the command of Sir Francis Drake, and fitted out at the joint cost of the queen, Hawkyns, Drake, and possibly other minor adventurers. After many delays this fleet left Plymouth in August 1595, by which time the Spaniards were well informed of its destination and its force. It thus disappointed expectation; but Hawkyns did not witness the failure. He died at sea off Porto Rico on 12 Nov. 1595. His death was doubtless due to the effect of the West Indian climate on a man no longer young, and with a constitution already weakened by former hardships and by attacks of fever and ague, one of which in 1581 had brought him to death's door (, p. 43n.) Four days before his death, feeling his strength failing, he added a last codicil to his will, in which, after directing restitution to be made to any man whom he had injured, he continued: ‘For the faults or offences which I have or might have committed against her Majesty, I do give unto her 2,000l. (if she will take it), for that she hath in her possession of mine a far greater sum which I do release unto her. This I mean with God's grace to perform myself, if he of his mercy send me home.’

Hawkyns was buried at sea, but in accordance with his will a monument was erected to his memory in the church of St. Dunstan's-in-the-East, in which parish he had resided for thirty years, and to the poor of which, as well as a Plymouth and of Deptford, he bequeathed a sum of 50l. In addition to the Latin inscription on the monument, another in English was shown on a mural tablet. These with the church perished in the great fire; but the inscriptions have been preserved