He married Mary Riley (c. 1804-1870) on 13 February 1834 in Gallia County, Ohio. They did not have any children.
John died c. 30 August 1860 in Greene County, Indiana, United States at the age of 54. There is a copy of his will dated 12 July 1860 in Greene County, Indiana. The probate of the will was on 30 August 1860. He left his wife Mary and Elsa Riley as executors and bequeathed to George Fry ...a boy whom I raised $300.
1840 United States Federal Census in Ohio Township, Gallia County, Ohio. Tally only for John L. Waugh with a household of 2. 1 male 30-39 and 1 female 30-39.
1850 United States Federal Census on 25 November in Ohio Township, Gallia County, Ohio. Family 96. 
1860 United States Federal Census on 9 August in Taylor, Greene, Indiana. Post office is in Scotland. Page 197, Lines 25-26. 
Jordan Dodd, Liahona Research. Ohio, Marriages, 1803-1900, page 241 for John Waugh and Mary Riley.
Marriage Records. Ohio Marriages. Various Ohio County Courthouses. Original in Gallia County by Justice of the Peace Franklin Card.
Indiana County, District and Probate Courts. Will Records, Probate Court, Vol. 2, 1856-1883 for John L. Waugh. Will 12 July 1860.
↑ 1850: Waugh, John L. 43 b. OH, farmer, head; Mary 46 b. Pennsylvania, wife; Fry, George 16, labor.
↑ 1860: Waugh, John L. 54, b. OH, farmer, head; Mary 88 (sic) birth year given as 1804 in PA, wife (she was 56); Fry,
George 24 (b. c. 1836 in OH), farm labor.
It may be possible to confirm family relationships with John by comparing test results with other carriers of his ancestors' Y-chromosome or mitochondrial DNA.
However, there are no known yDNA or mtDNA test-takers in his direct paternal or maternal line.
It is likely that these autosomal DNA test-takers will share DNA with John: