Lord Winton never made a recognised marriage. It was alleged, by a claimant to the Earldom, that he had married about 1710 Margaret McKlear; and while commonly known by many was never legally proved later. It is however certain from the evidence of documents and papers remaining that his mistress Elizabeth Stevenson had by him, a son John and a daughter Christian, and the Masonic records in Rome note that he was in fact married and that his wife passed on the records of the Lodge following his death.

The claimant was certainly descended from the son of the 5th Earl, by Margaret McKlear, as the correspondence in regard to the Earl's confinement in the Tower mentions a son Charles; but he has been regarded as being a 'natural son', again, since the marriage cannot be documentarily substantiated.

In the very rare printed pamphlet, in which this appears, she is said to have put forward some letters to her from a Mrs Corsbie "who was then attending the "said Earl" in prison. This woman had an alias "Margaret McKlear" . The Earl's solicitor Charles Menzies W.S. of the family of Menzies of St. Germains, also deponed that this lady "by favour of the "warders" had access to the Earl. She was also in London as a witness for the Earl.

On the 14th of January 1617 a charter of Aldingstone and Greendykes was granted to Sir John Seton and his mother ; and three and a half years later (3rd July 1620) he and his 'affidate spouse,' Margaret Kellie, had another charter of the lands of St. Germains from his brother George, third Earl of Winton. Again, on the 15th of February 1621, there is a charter by the King to ' John Seytoun of Sanct Germains ' of the lands and barony of Foulden, in the shire of Berwick, apprised from William Arnote of Cokburnespeth,
and sold to the said John Seytoun for 2500 merks, due to Mr. William Kellie, W.S.. Some nine years afterwards (31st December 1629) we find a registered discharge by Alexander, Earl of Eglinton, George, Earl of Winton, and Sir William Seton of Kylesmure, in favour of their 'beloved brother,' John Seton of St. Germains, from the obligation which he had granted to them and the late Margaret, Countess of Winton, in June 1620, not to sell his lands, in consideration that he was now of age to manage his own affairs.

Sir John Seton 'dyed in good age [July 1638], and was buried in the buriall place of Seton.' * This appears from the record of his ' Testament Testamentar' in the Edinburgh Register dated the 4th of July, 1638 written partly by himself and partly by Margaret Kellie, his relict spouse, wherein he constitutes Dame Margaret Kellie, his spouse, his only executrix and tutrix to his children. The free gear amounted to v°xxxiij lib , and Robert Seton of Monkmylne is a witness. He was buried at Seton Collegiate Church.