Adam Winthrop, John Winthrop's grandfather, was but a simple cloth merchant in London when in 1544 King Henry VIII decided to sever ties with the Catholic Church and form the Church of England. The king confiscated hundreds of properties from the Catholic Church and resold them at cut-rate auctions. Adam Winthrop saw a unique opportunity and paid about 408 pounds for an old monastery in Groton, outside London.

Over the next half century, as the manor became the focal point for the Winthrop family, all around them England underwent a religious upheaval. After Henry VIII died, the throne passed through several quick changes before settling on Elizabeth I, a protestant from the House of Tudor. In the years that followed, Elizabeth dealt with a country divided almost evenly between disenfranchised Catholics and reform-minded Protestants–all the while successfully fighting attempts by the Catholic King Philip II of Spain to invade England and recapture the throne for a Catholic.

The final blow to Philip's crusade came in May 1588, five months after John Winthrop was born. Philip sent more than 100 naval ships, nicknamed the Spanish Armada, into the English Channel, only to be beaten back by the combined English fleet and a horrible storm. The English rejoiced, knowing that God had intervened on their side and punished the Spanish with the tempest.

Thus, although the world in which John Winthrop was born on January 22, 1588 was a dangerous one, his homeland was safe before he could walk. Winthrop spent his first years in Edwardston, near the Groton estate. When John's father, Adam Winthrop, Jr. of Groton, inherited the manor after his father's death, Adam Jr. moved his family to the former monastery. The manor, set in the rolling fields and dark woods of Groton, was ideal for the young Winthrop. A large barn dominated the estate, with nearby buildings for the family and small ponds nearby for carp fishing.

Although schooled in law, John's father devoted his life to the running of the estate, which became increasingly difficult as an economic recession in the late sixteenth century pushed prices ever higher. English law fixed the rates that the Winthrop could charge tenants on the land, so the family was forced to look elsewhere for funds. Adam fixed on cash crops like wheat, barley and peas, since the manor was close enough to provide food for London. By the time John turned five, his father was earning sixty-two pounds a year from the manor's crops–a massive sum for the time and more than the Winthrops collected from all of the rental properties on the land.

The Winthrop family also welcomed a constant stream of family visitors through the house, including an uncle who had journeyed to Spain in order to kill the Catholic king but instead converted to Catholicism himself after meeting a Jesuit priest. Another uncle, who split his time between England and Ireland found himself excommunicated from the Church after failing to properly divorce one wife before marrying another. And although little is known of Anne Browne, John's mother, except that she was extremely pious protestant, the family atmosphere as a whole was undoubtedly open and exciting for young John Winthrop.

At age seven, Winthrop began his formal "scholinge" under the tutelage of John Chaplyn, the vicar of the local church. Coming from a Suffolk family, it was only fashionable that Winthrop would attend Cambridge University. Luckily, his father had been appointed auditor of Trinity College. Each November, Adam Winthrop would journey to Cambridge to audit the college's books, and in 1602 he had John–then fourteen–admitted to the school.

The transition to college the next spring was rough for Winthrop. He found himself homesick, writing, "I fell into a lingring feaver, which took away the comfort of my life." At the same time, he found himself taken with all the new sights of Cambridge, remarking that his "lusts were so masterly as no good could fasten upon me." He studied only two years, as was then customary. After all, the sons of gentlemen were supposed to help run the family. A year after returning to the Groton estate, Winthrop's father arranged for him to marry Mary Forth, the daughter of an Essex nobleman. On April 26, 1605, the two were married.

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