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He was the son of Sir John Throckmorton, the seventh out of eight sons of Sir George Throckmorton of Coughton Court. He was a nephew of Sir Nicholas Throckmorton, one of Elizabeth's diplomats, who had held the post of Chief Justice of Chester but was removed in 1579, a year before his death. His paternal grandmother, Hon. Katherine Vaux, daughter of Nicholas Vaux, 1st Baron Vaux of Harrowden, was the paternal aunt of the Protestant queen consort of King Henry VIII, Catherine Parr.
Francis Throckmorton was educated in Oxford and entered the Inner Temple in London as a pupil in 1576. In 1580, he traveled to the European continent and met leading Catholic malcontents from England abroad (in Spain and France). It was in Paris that Throckmorton met Charles Paget and Thomas Morgan, agents of Mary, Queen of Scots. Following his return to England in 1583, he served as an intermediary for communications between supporters of the Catholic cause on the continent, the imprisoned Mary, Queen of Scots, and the Spanish ambassador Bernardino de Mendoza.
His activities raised the suspicions of Sir Francis Walsingham, Elizabeth I's spymaster. A search of his house produced incriminating evidence and, after torture on the rack, Throckmorton confessed his involvement in a plot to overthrow the Queen and restore the Catholic Church in England. An invasion led by Henry I, Duke of Guise, would have been coupled with an orchestrated uprising of Catholics within the country.
Sir Francis Throckmorton is featured in the film Elizabeth: The Golden Age, where he is played by Steven Robertson. In the film, he is shown asking for help from his cousin, Elizabeth Throckmorton, one of Queen Elizabeth's ladies-in-waiting and later the wife of Sir Walter Raleigh.
- Debrett's Peerage, 1968, p.792
- Stephen Budiansky. Her Majesty's Spymaster: Elizabeth I, Sir Francis Walsingham, and the Birth of Modern Espionage, Penguin, Jul 25, 2006. pg 123-139.
- Chisholm 1911.
- Chisholm, Hugh, ed. (1911). "Throckmorton, Francis". Encyclopædia Britannica. 26 (11th ed.). Cambridge University Press. p. 891.
- Lee, Sidney (1898). "Throckmorton, Francis". In Lee, Sidney. Dictionary of National Biography. 56. London: Smith, Elder & Co.
- Plowden, Alison. "Throckmorton , Francis (1554–1584)". Oxford Dictionary of National Biography (online ed.). Oxford University Press. doi:10.1093/ref:odnb/27390. (Subscription or UK public library membership required.)
- Butler, Charles (1822). "The Treason of Francis Throckmorton". Historical Memoirs of the English, Irish, and Scottish Catholics, Since the Reformation. pp. 376–377. OCLC 588795283.