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The company of Massachusetts was originally designed to be, like that of Virginia, a corporation established in England administering the affairs of an American colony. But on 28 July 1629 Matthew Cradock, governor of the Massachusetts Company, at a meeting held at the house of the deputy-governor, Thomas Goffe, in London, read certain propositions conceived by himself, giving reason for transferring the government from the council in London to the plantation itself. The authorities at Salem, now of several years' standing, had hitherto been subordinate to those of the company at home; on 26 Aug. 1629, at a meeting held at Cambridge, John Winthrop was one of the twelve signatories (including the names of Richard Saltonstall [q. v.], Thomas Dudley [q. v.], William Vassall [q. v.], Increase Nowell [q. v.], and William Pynchon [q. v.], all of whom are separately noticed) to an agreement by which the framers pledged themselves to set sail with their families to ‘inhabit and continue in New England, provided that the whole government, together with the patent for the plantation, be first by an order of court legally transferred and established, to remain with us and others which shall inhabit upon the said plantation.’ On 20 Oct. it was announced by the court of the company that the transference of the government had been decided upon, and that same day, from among four nominees, John Winthrop was by general vote and show of hands chosen to be governor for the ensuing year.

After some five months of preparation, on 22 March 1629–30 four ships out of the eleven that the emigrants had chartered were ready to sail from Southampton, and upon that day Winthrop embarked with Saltonstall, and with Thomas Dudley, William Coddington [q. v.], and Simon Bradstreet [see under Bradstreet, Anne], upon the principal ship, the Arbella. Two of his younger children were with him, but his wife was obliged by reason of her pregnancy to postpone her departure for a little over a year. Winthrop and his comrades were delayed by contrary winds off the Isle of Wight for a fortnight, and they took the opportunity to promulgate the notable ‘letter of farewell’ to their fellow-countrymen, entitled ‘The Humble Request of his Majesty's Loyall Subjects, the Governor and the Company, late gone for New England, to the rest of their brethren in and of the Church of England, for the obtaining of their Prayers and the removal of Suspicions and misconstruction of their Intentions.’ While still at ‘the Cowes’ Winthrop also commenced that diary or journal (see below) which was continued thenceforth until the close of his career, and was destined to form the staple of all subsequent histories of the infant colony of New England. In the course of the voyage, which proved a tedious one, Winthrop further wrote a little work of edification entitled ‘Christian Charitie. A Modell hereof.’ The manuscript was presented to the New York Historical Society by Francis B. Winthrop, a lineal descendant of the author, and in 1838 it was printed by the Massachusetts Historical Society (Collections, 1838, 3rd ser. vii. 31).

After a voyage of sixty-six days the Arbella and her consorts came to an anchor in the harbour of Salem. On 17 June 1630 (O.S.) Winthrop definitely decided upon Charlestown (now the northern suburb of Boston) in preference to Salem as a residence. Here he was welcomed by John Endecott [q. v.], who made over to him the authority which he had exercised as acting governor since September 1628. The colony, which (exclusive of the Mayflower emigrants of Plymouth plantation, not incorporated in Massachusetts until 1691) numbered barely three hundred souls, was now increased at a bound to between two and three thousand. Winthrop drew up a church covenant on 30 July, and some five weeks later was driven by lack of water to quit Charlestown and to establish his headquarters upon the neighbouring peninsula of Shawmut, to which the name of Boston was given. A general court (the second) was held at Boston on 18 May 1631, when Winthrop was re-elected governor, and a most important decision was arrived at, to the effect that ‘for time to come no man shall be admitted to the freedom of the body politic but such as are members of some of the churches within the limits of the same.’ In May 1632 Winthrop was re-elected governor, and shortly after this date, in a letter from Captain Thomas Wiggin to Secretary Coke, we have a brief picture of the plantation and its chief ruler. The English there, ‘numbering about 2,000, and generally most industrious, have done more in three years than others in seven times that space, and at a tenth of the expense. They are loved and respected by the Indians, who repair to the governor for justice. He [John Winthrop] is a discreet and sober man, wearing plain apparel, assisting in any ordinary labour, and ruling with much mildness and justice’ (Cal. State Papers, Colonial, 1574–1660, p. 156). In September 1632, in his capacity as governor, Winthrop paid a ceremonious visit to the planters at Plymouth. About this same period an animated quarrel between the governor and his deputy, Thomas Dudley, was allayed