In 1880, the family was living in Cove, Polk County, Arkansas.
On March 14, 1889 he married Mollie Campbell in Polk County, Arkansas. 
John, his wife and five children are found residing in Holly Creek, Wayne County, Arkansas in 1900. He is listed as being 32 years of age, born January 1868 in Arkansas. 
FamilySearch has that his date of birth is Jun 1869 on the 1900 census but it is a transcription error, if you look at the census record it clearly has Jan 1868.
↑ "United States Census, 1880," database with images, FamilySearch (https://familysearch.org/ark:/61903/1:1:MNWK-MF2 : 13 August 2016), John D Williams in household of Thomas Williams, Cove, Polk, Arkansas, United States; citing enumeration district ED 128, sheet 526C, NARA microfilm publication T9 (Washington D.C.: National Archives and Records Administration, n.d.), roll 0054; FHL microfilm 1,254,054.
↑ "United States Census, 1900," database with images, FamilySearch (https://familysearch.org/ark:/61903/1:1:M3FQ-TN6 : accessed 29 September 2018), Mary E Williams in household of John D Williams, Blue Ridge, Holly Creek & Sulphur Springs Townships, Howard, Arkansas, United States; citing enumeration district (ED) 66, sheet 3A, family 46, NARA microfilm publication T623 (Washington, D.C.: National Archives and Records Administration, 1972.); FHL microfilm 1,240,061
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It may be possible to confirm family relationships with John by comparing test results with other carriers of his Y-chromosome or his mother's mitochondrial DNA.
Y-chromosome DNA test-takers in his direct paternal line on WikiTree: