Born in Turkey Creek, Tennessee to Col. William Fly and his wife, Mary Mitchell Fly, John Dalton Fly migrated south to MS where he first married Martha Irven Divine, daughter of Kinsman & Elizabeth Divine of Jefferson Co., MS. They had one son, William Kinsman Fly (1845-1881). Martha apparently died in childbirth in 1845. She is buried in the churchyard of the Sharon Church in Madison Co. MS.

Next he was married for a second time to Julia Fletcher Stokes, a widow with two young children (1824-1865) on July 4, 1848. They had seven children together. By the 1860 Census, they were living in Big Hill, Gonzales, Texas. Julia died in 1865 in Texas.

John Dalton married for a third time to Eleanor Virginia "Nora" Compton on 15 March 1866. Nora's family had a plantation in Madison County, Mississippi which is where the MS Marriage Records show that the marriage took place. However, there is also a Texas Marriage Collection record showing that they married on that same day in Washington, Texas. John Dalton and Nora had one child together.

On 19 Mar 1867, their only known child together, Thomas Compton Fly, was born in Gonzales, TX and was named after his maternal grandfather, Thomas Alexander Compton.

The next found record on them shows them in Refugio, TX in the 1870 Census. The 1880 Census found them in Gonzales, TX.

Dec. 1, 1884 was the given death of their son, Thomas Compton Fly in Texas. He was just 17.

Some family trees give John Dalton Fly's place of death as Canton, Madison County, MS. This would be logical since his family had settled here after leaving Tennessee. Nora is known to have then moved to Oxford, Layfatte Co., MS to live with two of her sisters and a niece. Her late husband is definitely buried there. Nora is documented in the 1900 Census there. Family tradition says she died and was buried in Oxford, Lafayette County, MS but no record of her burial place has been found as of 2024.