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A native of Northamptonshire, Knolles was born in the 1540s, probably at Cold Ashby. He was educated at Lincoln College, Oxford, where he graduated with a BA in January 1565. Knolles then became a fellow at Lincoln College, and obtained his MA there in July 1570. Some time after 1571, he left Oxford to become headmaster at a grammar school in Sandwich, Kent, which was founded by Sir Roger Manwood circa 1563.
After Manwood’s death in 1592, his son, Sir Peter became Knolles’ professional and literary patron and encouraged Knolles to write. In 1603, Knolles published his Generall Historie of the Turkes, of which several ions subsequently appeared, among them Sir Paul Rycaut's ion (1700). Rycaut’s ion includes his account of his time in Constantinople as secretary to the English ambassador. While the topic of the Turks was very popular during the period in which Knolles wrote, with an estimated 1,000 works about the Turks published in Europe between 1501 and 1550, Knolles’ history was the first chronicle of the military and political aspects of the Ottoman Empire to be written in English. Previous histories had been available only in Latin and were thus not widely circulated. Knolles also published a composite translation of Jean Bodin's Les Six livres de la République in 1606 under the title, The Six Bookes of a Commonweale; it is based on both the French and Latin versions of Bodin's text and was dedicated to Sir Peter Manwood. Knolles also worked on an unpublished translation of Camden’s Latin original, Britannia. Though unpublished, Knolles' third work survives in the Bodleian Library at the University of Oxford.
His work had considerable merits of style and of arrangement. Samuel Johnson praised Knolles as the best of English historians, saying that "in his history of the Turks [Knolles] has displayed all the excellencies that narration can admit." Johnson explained Knolles' limited reputation by pointing out that his history recounted "enterprizes and revolutions, of which none desire to be informed".
Knolles died in Sandwich in July 1610, and was buried in St. Mary’s church.
Publishing dates for the ions of The Generall Historie of the Turkes
1603 – original ion
1621 – includes continuation by Edward Grimestone
1631 – includes continuation by Sir Thomas Roe, English Ambassador in Constantinople
1700 – Sir Paul Rycaut ion
1701 – two-volume abridged ion by John Savage