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John Allen Ware was one of two children, the only son, born to Eli Ware, a pioneer school teacher, native of Spartanburg, South Caroliona, and Elizabeth Hinton Vinson Vinson born in Tennessee, a young woman of means.

Eli Ware came to Rusk, Texas when it was a part of Mexico in late 1830s. Eli purchased his first land in 1842. Rusk was taken from part of Nacogdoches County to become a county in 1843.

Eli believed in education for the children, and taught them in a small one room school house. He taught school about four months of the year. The children were needed on the farms to help their parents with crops and worked hard the rest of the year. Eli War eventually started a tannery which provided a decent income. He kept purchasing land until he owned about 8000 acres. He built a log house on part of his vast acreage.

Eli Ware and the young woman he loved, Elizabeth Hinton Vinson married about 1849.

They had two children, Sallie Ware and John Allen Ware.

Eli cleared some of his land and was preparing to build Elizabeth a larger house. Tragedy struck their lives when Eli suddenly became ill and died.

His wife Elizabeth was left bereft, and had her two young children to care for. The following year she married widower James Winright Flanagan, a strong, powerful, industrious man who was Lt. Governor of Texas in 1869, and U.S. Senator from Texas 1870 -1875. He was a devout Christian man of the Baptist faith.

John Allen Ware grew up as a son of James Winright Flanagan. John Allen Ware and Horace Bell Flanagan, called Bell Flanagan, knew each other from childhood. Her father, General Webster Flanagan, was a son of James Winright Flanagan. John and Bell Flanagan married. They later moved to Longview, Gregg County, the next county over from Rusk County, Texas, where they settled and raised their family of several children.