1593 -- He was baptized at Naughton, Suffolk, England.
He was one of three sons of the clergyman Thomas Stoughton (c.1557 - c.1622) and Katherine Evelyn Stoghton (c.1560 - c.1603). 
1606 -- John's father, Thomas, lost his living of Coggeshall, Essex, England because he was a nonconformist.
John's brothers were Thomas and Israel Stoughton. 
1607 - 1626 -- John was a student at Emmanuel College, Cambridge, graduating with a B.A. in 1611, an M.A. in 1614, a B.D. in 1621, and a D.D. in 1626.
1616 -- John became a Fellow at Aller in Somersetshire, England.
1624 - 1632 -- John became Rector at Aller in Somersetshire, England. 
1632 on -- John preached at St. Mary, Aldermanbury, in London.
1624 -- Stoughton's predecessor at Aller, Ralph Cudworth (the elder), died. 
1624 -- John married Mary Machell Cudworth, widow of Ralph Cudworth. Mary Machell had formerly been the nurse of Henry Frederick, Prince of Wales.   John became the stepfather of Ralph Cudworth (the younger) and James Cudworth. John educated Ralph. James emigrated to New England.
1636 -- he married Jane Browne, widow of Walter Newburgh, and daughter of John Browne. 
His brother Israel Stoughton was a co-worker with John Endicott in Massachusetts Bay Colony. Their correspondence is available at  John's nephew and Israel's son, "William Stoughton, [was] chief magistrate of the Salem witch trials." 
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