Sir John Wattson (died 1616) was an English merchant and shipowner, active in the East India Company and Virginia Company and Lord Mayor of London in 1606.
The son of Thomas Watts of Buntingford, Hertfordshire, he was owner of the Margaret and John, one of the ships paid by the city of London in 1588 to sail against the Spanish armada. Watts himself served in her as a volunteer, and saw action. In 1590 the same ship was one of a fleet of merchantmen coming home from the Mediterranean, which fought and beat off Spanish galleys near Cadiz. Although Watts was not on board, throughout the war he equipped and financed privateers led by Michael Geare, William Lane and Christopher Newport. A few of his notable successes include his financed and organised expedition to the Spanish main in 1590, the expedition to Cuba the following year and James Lancaster's expedition to Recife in April 1595. Watt's received significant prize money from the success of the expeditions. Another in July 1601 took into Plymouth a prize coming from the Indies laden with China silks, satins, and taffetas. At this time he was an alderman of London (Tower ward), and had been suspected of being a supporter of Robert Devereux, 2nd Earl of Essex.
He was one of the founders of the East India Company, and on 11 April 1601 was elected its governor, during the imprisonment of Sir Thomas Smythe. He served as a Sheriff of the City of London in 1597. On the accession of James I he was knighted on 26 July 1603, becoming Lord Mayor of London in 1606–1607, at which time he was described in a letter to the king of Spain as "the greatest pirate that has ever been in this kingdom". During the following years he was an active member of the Virginia Company. In the city of London, Watts was a member of the Clothworkers' Company.